- Rnatoolbox-help - SimTK Mailing Lists

tried Installer.3_0.OSX, fails on Ventura 13.6 Intel
by Bert Gold 09 Nov '23

09 Nov '23

Hello, This version fails to pass the security checks. Especially the libsimTKxxxxx.dylib I cannot run MMB without them. What version succeeds on Ventura? -- Bert Gold Falmouth, MA 302-507-1827

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Re: distro
by Samuel Flores 19 Mar '15

19 Mar '15

On Mar 19, 2015, at 12:36 AM, Alex Tek <alex.tek.fr(a)gmail.com> wrote: >> As I understand your code, you first create a wrapper struct whose members look like the ParameterReader members. Then you have functions to copy from the ParameterReader to the wrapper and back, all in c++. Then in params.py you have a python version of the wrapper, which I think is perhaps hard coded to directly access the wrapper. >> >> The wrappers add a bit of risk of bugs since changes have to be made in multiple places. Is there any way this could be avoided? Is it possible to use SWIG? > Yes SWIG is probably a good solution. It seems to me that you are doing more than just translating c++ headers to c. the updateParameterReader_wrapper method has no equilivalent in ParameterReader.cpp, for instance. So SWIG might involve doing things very differently, compared to what we are doing currently. > In the meantime, update share and check genCtypesStructs.py. I fixed it to make it generate proper wrappers, but only for ParameterReader. So you made an automated wrapper generator! very impressive. It’s spitting out a bunch of errors though, appended below. Or are these just warnings? It seemed to compile fine anyway. either way I think we’re done with the mmb.pdb issue. Thanks for your help. > Usage: python share/genCtypesStructs.py include/ParameterReader.h include/ParameterReader_wrapper.h share/pyMMB/params.py > (you have to be at the root of the project). > In the past, I used this script for the classes and structs in utils.h. But it doesn't produce ready to use wrappers. This is probably broken now anyway. >> >> Alternatively, would it not be better, if the params.py were linked hard to ParameterReader rather than its wrapper? I don’t see that there is any validation happening, which would be one reason to have ParameterReader_wrapper.h. Is this possible? Bear in mind I’m a python amateur. > No, unfortunately you can't do that. Python can execute C functions, but not C++. Indeed, once compiled, C++ method names are modified (see C++ name mangling for more info), making it unreliable to be wrapped. > This is why we have these wrappers. Notice that the code of python_wrapper.cpp is wrapped inside an extern "C" declaration, marking it as C code for programs using the library. Note that only the signature of the functions has to follow the C rules. Their guts can totally use c++, and this is what we do here. > > And actually, python_wrapper.cpp is quite ill named as it is really a C wrapper. The python wrappers are in wrappers.py. > SWIG is doing the same thing, except that it's automatized. >> >> samuel-floress-macbook-pro-3:trunk Sam$ python share/genCtypesStructs.py include/ParameterReader.h include/ParameterReader_wrapper.h share/pyMMB/params.py Unknown type: // ParameterReader & operator = (const ParameterReader in ParameterReader Unknown type: ErrorManager & in ParameterReader Unknown type: // in ParameterReader Unknown type: vector<CovalentBondClass> in ParameterReader Unknown type: vector<IncludeIntraChainInterface> in ParameterReader Unknown type: BasePairContainer in ParameterReader Unknown type: map<const ChainResidueIndex, BasePairPartner,twoIndexCmp> in ParameterReader Unknown type: // variables previously declared and initialized in in ParameterReader Unknown type: //bool in ParameterReader Unknown type: //bool in ParameterReader Unknown type: //String in ParameterReader Unknown type: //bool in ParameterReader Unknown type: //int in ParameterReader Unknown type: //int in ParameterReader Unknown type: BondMobility::Mobility in ParameterReader Unknown type: BondMobility::Mobility in ParameterReader Unknown type: BondMobility::Mobility in ParameterReader Unknown type: BondMobility::Mobility in ParameterReader Unknown type: Vector in ParameterReader Unknown type: LeontisWesthofClass in ParameterReader Unknown type: // end of variables improted from in ParameterReader Unknown type: //int in ParameterReader Unknown type: //int in ParameterReader Unknown type: //vector<Biopolymer> in ParameterReader Unknown type: //vector<String> in ParameterReader Unknown type: vector<int> in ParameterReader Unknown type: map<const ChainResidueIndex, int,twoIndexCmp> in ParameterReader Unknown type: //vector<double> in ParameterReader Unknown type: //vector<int> in ParameterReader Unknown type: //vector<double> in ParameterReader Unknown type: //vector<int> in ParameterReader Unknown type: /*vector<double> in ParameterReader Unknown type: vector<int> in ParameterReader Unknown type: vector<double> in ParameterReader Unknown type: vector<int> in ParameterReader Unknown type: LeontisWesthofClass in ParameterReader Unknown type: mutable map<const String,double> in ParameterReader Unknown type: DensityMap in ParameterReader Unknown type: DensityMap in ParameterReader Unknown type: MobilizerContainer in ParameterReader Unknown type: PhysicsContainer in ParameterReader Unknown type: ConstraintToGroundContainer in ParameterReader Unknown type: DisplacementContainer in ParameterReader Unknown type: AtomSpringContainer in ParameterReader Unknown type: BiopolymerClassContainer in ParameterReader Unknown type: MoleculeClassContainer in ParameterReader Unknown type: WaterDropletContainer in ParameterReader Unknown type: map<const String,String> in ParameterReader Unknown type: map<const String,String> in ParameterReader Unknown type: map<const String, int> in ParameterReader Unknown type: map<const String,int>::iterator in ParameterReader Unknown type: // //void addRingClosingBond(const String chainID, ResidueID residueID1, String atomName1,String bondCenterName1, ResidueID residueID2, String atomName2,String in ParameterReader Unknown type: // void addC1pSprings (LeontisWesthofClass in ParameterReader Unknown type: // void applyAtomSprings (SimbodyMatterSubsystem & matter, GeneralForceSubsystem & in ParameterReader Unknown type: // void configureDumm( DuMMForceFieldSubsystem & in ParameterReader Unknown type: // static double myAtoF(map<const String,double> myUserVariables,const char* value in ParameterReader Unknown type: // static bool aToBool( const String& name, const char* value in ParameterReader Unknown type: // static bool compareUpper( const String& param, const char* symbol in ParameterReader Unknown type: vector<BasePair> in ParameterReader Unknown type: ContactContainer in ParameterReader Unknown type: DensityContainer in ParameterReader Unknown type: DensityContainer in ParameterReader Unknown type: vector<SingleBondMobility> in ParameterReader Unknown type: vector<BasePairPartner> in ParameterReader Unknown type: //vector<IncludeAllNonBondAtomsInResidue> in ParameterReader Unknown type: vector<AllResiduesWithin> in ParameterReader Unknown type: vector<IncludeNonBondAtomInBiopolymerStruct> in ParameterReader Unknown type: vector <WaterDropletAboutResidueStruct> in ParameterReader Unknown type: vector<MobilizerDomainsInterface> in ParameterReader Unknown type: // void removeBasePairsInRigidStretch in ParameterReader Unknown type: // void printAllSettings ( ostream & myOstream = std::cout, String remarkString = in ParameterReader Unknown type: // void removeNonPriorityBasePairs (int in ParameterReader Unknown type: // //int getFirstResidueNumbers(const String myChainId) in ParameterReader Unknown type: // // int getProteinFirstResidueNumbers(const String myProteinChainId) in ParameterReader Unknown type: // //int getBasePriority(int baseResidueNumber,String baseChain, String basePairingEdge) in ParameterReader Unknown type: // // int getNumBasePairs() in ParameterReader Unknown type: // void addAllResiduesWithin(String chainID, int resID, double in ParameterReader Unknown type: // void updateAllResiduesWithin(int index, String chainID, int resID, double in ParameterReader Unknown type: // void deleteAllResiduesWithin(int in ParameterReader Unknown type: // void updateIncludeAllNonBondAtomsInResidue(int index, String chainID, int in ParameterReader Unknown type: // void deleteIncludeAllNonBondAtomsInResidue(int in ParameterReader Unknown type: // //int in ParameterReader Unknown type: // //int calcLowestBondingResidue(const String in ParameterReader Unknown type: // //int calcHighestBondingResidue(const String in ParameterReader Unknown type: // void in ParameterReader Unknown type: // void parameterStringInterpreter(const String & in ParameterReader Unknown type: // void initializeFromFileOnly(const char * parameterFileName = "./commands.dat" in ParameterReader Unknown type: // void setFirstAndLastStage(const char * parameterFileName = "./commands.dat" in ParameterReader Unknown type: // void loadSequencesFromPdb(const char * in ParameterReader Unknown type: // //void in ParameterReader Unknown type: // // void in ParameterReader Unknown type: // // void in ParameterReader Unknown type: // void in ParameterReader Unknown type: // void in ParameterReader Unknown type: // void in ParameterReader Unknown type: // void in ParameterReader Unknown type: // void in ParameterReader Unknown type: // // void initializeDefaults in ParameterReader Unknown type: // void initializeDefaults(const char * leontisWesthofInFileName = in ParameterReader Unknown type: // void initialize(const char * parameterFileName = "./commands.dat" in ParameterReader Unknown type: // //bool chainIsBiopolymer(String myChainId in ParameterReader Unknown type: // //bool chainIsMonoAtoms(String in ParameterReader Unknown type: // //int getChainIndex(String myChainId , vector<Biopolymer> & in ParameterReader Unknown type: MonoAtomsContainer in ParameterReader Unknown type: //dutyCycle = in ParameterReader Unknown type: //priority = in ParameterReader samuel-floress-macbook-pro-3:trunk Sam$

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Re: mmb
by Samuel Flores 10 Dec '14

10 Dec '14

Hi Adelene, You’re right, the example threads a little messily. I’ve fixed this for the next release (2.16). I made the following changes: 1. Threaded to one additional residue on the template. 2. Used “physics where you want it” rather than the contact command to prevent steric clashes. This will spread out the loop nicely, and is just better all around (uses PARM99). 3. Shifted the template so it’s less likely to tangle. There are other ways to get out of kinetic traps, but for a simple example I thought we’d go this way. 4. Shortened the simulation time. You don’t need to run for 500 steps. I’ve attached the updated PDB and command file. Sam On Dec 9, 2014, at 10:56 PM, Adelene Sim <adelenes(a)bii.a-star.edu.sg> wrote: > Hi Sam, > > I'm having some trouble with threading on MMB and was wondering if you can help me take a quick look. Basically I'm following the tutorial and trying to do RNA threading. Turns out my RNA doesn't look right and there appears to be lots of clashes even though I followed the tutorial's input. I tried to run for longer just to see if it'll equilibrate but sadly it didn't! > > The input, output and final trajectory file can be downloaded from here: https://www.dropbox.com/sh/tx9hpvw772h3hz0/AABnj-_n0lAbLijD9ZLBJwz4a?dl=0 > > From looking at the trajectory it appears as if the sterics component is not implemented and the RNA gets very distorted. I used the Mac binary downloaded from SimTK. > > I know you're busy so I really appreciate it if you can take a look! Thanks! > > Adelene > > On 25/11/14 6:23 AM, Samuel Flores wrote: >> You have been contacted by a member of Simtk.org. >>

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Re: MMB issues
by Samuel Flores 25 Mar '14

25 Mar '14

On Mar 25, 2014, at 12:06 PM, Erik Marklund <erik.marklund(a)chem.ox.ac.uk> wrote: > Hi Sam, > > How are things with you? Do I remember correctly that you've entered parenthood nowadays? Yes! > > I indended to use MMB for filling in a gap in a loop, just a single amino acid. Sounds trivial, but I can't get it to work. The protein looks like someone set of a bomb in the middle of it already at frame 1. Could you spot any obvious error in this input file below? The protein is a homodimer with a single amino acid missing at position 49. The problem is that you are instantiating the chains directly using the “protein” command. This automatically assigns sequential residue numbers based on the provided sequence, starting in this case with “2”. You should instead read the sequences from the PDB — this will conserve the residue numbering in the PDB file, including all gaps and insertions. Then to add the residue, use the “insertResidue” command. I’ve provided the commands for inserting a tryptophan below (just put your structure in last.1.pdb). Also, are you using MMB 2.13? This probably won’t work with earlier revisions. Also, could you post such questions on the MMB forum on simtk.org, or to the rnatoolbox-help(a)simtk.org list? Can we put this one there? That way others will benefit. firstStage 2 lastStage 2 loadSequencesFromPdb insertResidue A 49 W I sent you an email some months ago about a new feature that constrains backbone dihedrals on one stretch of residues to be identical to that on another stretch. Is that still something you want to use? Sam > > firstStage 2 > lastStage 2 > reportingInterval 1 > numReportingIntervals 2 > > temperature 1.0 > # 0 10 20 30 40 50 60 70 80 90 > # | | | | | i| | | | | > protein A 2 STPADVKEHPNSYVFMVDMPGVKSGDIKVQVEDENVLLISGERKREEEKEGVKYLKMERRIGKLMRKFVLPENANIEAISAISQDGVLTVTVN > protein B 2 STPADVKEHPNSYVFMVDMPGVKSGDIKVQVEDENVLLISGERKREEEKEGVKYLKMERRIGKLMRKFVLPENANIEAISAISQDGVLTVTVN > > mobilizer Rigid A 2 47 > mobilizer Rigid A 52 94 > > mobilizer Rigid B 2 47 > mobilizer Rigid B 52 94 > > constraint A 2 weld B 2 > > contact AllHeavyAtomSterics A 2 94 > contact AllHeavyAtomSterics B 2 94 > > > Kind regards, > Erik > > > Erik Marklund, PhD > Postdoctoral Research Associate > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ >

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Re: About the cross the strand of RNA
by Samuel Flores 05 Oct '13

05 Oct '13

Hi Sung-Huan, I think you just needed to increase baseInteractionScaleFactor. The base pairing forces were not strong enough to overcome the backbone repulsion. I have appended a command file that works (see below your last message below). I am again cc'ing the help list. Samuel > Dear Samuel Flores, > > I try to set includeAllNonBondAtomsInResidues in my command. But I got a structure like a ring > > I just put includeAllNonBondAtomsInResidues in global and open electronic and vdw force. > # Sam's solution: #sequence RNA A 1 CAAAAGUCUGGGCUAAGCCCACUGAUGAGCCGCUGAAAUGCGGCGAAACUUUUG # stages firstStage 3 lastStage 4 #general simulation parameters baseInteractionScaleFactor 2000 reportingInterval .04 readFromStage 3 reportingInterval .4 numReportingIntervals 200 readBlockEnd temperature 20 randomizeInitialVelocities TRUE #base pairing forces to generate the hairpin baseInteraction A 1 WatsonCrick A 54 WatsonCrick Cis baseInteraction A 2 WatsonCrick A 53 WatsonCrick Cis baseInteraction A 3 WatsonCrick A 52 WatsonCrick Cis baseInteraction A 4 WatsonCrick A 51 WatsonCrick Cis baseInteraction A 5 WatsonCrick A 50 WatsonCrick Cis baseInteraction A 6 WatsonCrick A 49 WatsonCrick Cis baseInteraction A 7 WatsonCrick A 48 WatsonCrick Cis baseInteraction A 9 WatsonCrick A 21 WatsonCrick Cis baseInteraction A 10 WatsonCrick A 20 WatsonCrick Cis baseInteraction A 11 WatsonCrick A 19 WatsonCrick Cis baseInteraction A 12 WatsonCrick A 18 WatsonCrick Cis baseInteraction A 13 WatsonCrick A 17 WatsonCrick Cis baseInteraction A 29 WatsonCrick A 44 WatsonCrick Cis baseInteraction A 30 WatsonCrick A 43 WatsonCrick Cis baseInteraction A 31 WatsonCrick A 42 WatsonCrick Cis baseInteraction A 32 WatsonCrick A 41 WatsonCrick Cis setDefaultMDParameters > > 2013/10/4 Sung-Huan Yu <sunghuanyu(a)gmail.com> > Ha, I am stupid. includeAll"NonBond"AtomsInResidues. Sorry to bother you. > > > 2013/10/4 Sung-Huan Yu <sunghuanyu(a)gmail.com> > sorry, I would like to make sure one thing. Are the range of the command "includeAllNonBondAtomsInResidues" the helix part or loop part? > > > 2013/10/4 Sung-Huan Yu <sunghuanyu(a)gmail.com> > Dear Samuel Flores, > > Thank you for your reply. the following is my command. Actually, I try to use the software only two weeks. I tried "Physics where you want it" before. However, I got a structure like a big curve, the basepairing interaction can't work. Maybe I can try again. > > Now, I am a PhD student in IMIB of university of Wuerzburg. > > #sequence > RNA A 1 CAAAAGUCUGGGCUAAGCCCACUGAUGAGCCGCUGAAAUGCGGCGAAACUUUUG > > # stages > firstStage 1 > lastStage 2 > > #general simulation parameters > baseInteractionScaleFactor 20 > reportingInterval 4.0 > temperature 20 > randomizeInitialVelocities TRUE > #base pairing forces to generate the hairpin > baseInteraction A 1 WatsonCrick A 54 WatsonCrick Cis > baseInteraction A 2 WatsonCrick A 53 WatsonCrick Cis > baseInteraction A 3 WatsonCrick A 52 WatsonCrick Cis > baseInteraction A 4 WatsonCrick A 51 WatsonCrick Cis > baseInteraction A 5 WatsonCrick A 50 WatsonCrick Cis > baseInteraction A 6 WatsonCrick A 49 WatsonCrick Cis > baseInteraction A 7 WatsonCrick A 48 WatsonCrick Cis > baseInteraction A 9 WatsonCrick A 21 WatsonCrick Cis > baseInteraction A 10 WatsonCrick A 20 WatsonCrick Cis > baseInteraction A 11 WatsonCrick A 19 WatsonCrick Cis > baseInteraction A 12 WatsonCrick A 18 WatsonCrick Cis > baseInteraction A 13 WatsonCrick A 17 WatsonCrick Cis > baseInteraction A 29 WatsonCrick A 44 WatsonCrick Cis > baseInteraction A 30 WatsonCrick A 43 WatsonCrick Cis > baseInteraction A 31 WatsonCrick A 42 WatsonCrick Cis > baseInteraction A 32 WatsonCrick A 41 WatsonCrick Cis > > readAtStage 1 > numReportingIntervals 70 > readBlockEnd > > # During stage 2, do a de-tangling and de-clashing run. > # Remember, there is a stochastic element .. you may need to run this more than once to get convergence. > readAtStage 2 > # All forces (including base pairing and collision-detecting sphere forces) are inactive for scrubberPeriod*(dutyCycle-1) picoseconds, and active for scrubberPeriod*dutyCycle picoseconds. Note that dutyCy > cle defaults to 1.0: > dutyCycle 1.0 > scrubberPeriod 70 > constraint A 1 Weld A 54 > constraint A 2 Weld A 53 > constraint A 3 Weld A 52 > constraint A 4 Weld A 51 > constraint A 5 Weld A 50 > constraint A 6 Weld A 49 > constraint A 7 Weld A 48 > constraint A 9 Weld A 21 > constraint A 10 Weld A 20 > constraint A 11 Weld A 19 > constraint A 12 Weld A 18 > constraint A 13 Weld A 17 > constraint A 29 Weld A 44 > constraint A 30 Weld A 43 > constraint A 31 Weld A 42 > constraint A 32 Weld A 41 > constraintTolerance .001 > > numReportingIntervals 280 > # add collision-detecting steric spheres to all atoms except hydrogen. Note that the radius and stiffness of these spheres is set with the excludedVolumeRadius and excludedVolumeStiffness parameters: > contact AllHeavyAtomSterics A > # a higher temperature is good for thermal exploration > temperature 30 > readBlockEnd > > > > 2013/10/4 Samuel Flores <samuelfloresc(a)gmail.com> > Hi Sung-Huan > > I'm cc'ing the help list since there's nothing particularly private here -- let me know if you prefer not to. > > "Physics where you want it" is now much faster. I much prefer to use than now, rather than the "contact" commands. The command you want is probably "includeAllNonBondAtomsInResidues." You'll find it in the reference guide. > > You can also send me your command file if you want me to take a quick look. > > What university do you work at, out of curiosity? > > Sam > > > > > On Oct 4, 2013, at 5:37 PM, Sung-Huan Yu <noreply(a)simtk.org> wrote: > > > You have been contacted by a member of Simtk.org. > > > > From: Sung-Huan Yu > > Email: sunghuanyu(a)gmail.com > > > > The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff. > > > > > > *** MESSAGE BEGINS *** > > > > Hi, > > > > Recently, I try to simulate RNA 3d structure from sequence. However, I usually get the results of strand crossing. I mean the one strand pierce through another strand ( it is very clear to see in New cartoon presentation). Therefore, they will aggregate together. Could you give me some suggestions to set some parameters to avoid this situation? I already try some parameters about atom steric. it will make the basepairings become wrong. I also tried some numbers of the baseInteractionScaleFactor. it still not works. Thank you > > > > >

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Re: About the cross the strand of RNA
by Samuel Flores 04 Oct '13

04 Oct '13

Hi Sung-Huan I'm cc'ing the help list since there's nothing particularly private here -- let me know if you prefer not to. "Physics where you want it" is now much faster. I much prefer to use than now, rather than the "contact" commands. The command you want is probably "includeAllNonBondAtomsInResidues." You'll find it in the reference guide. You can also send me your command file if you want me to take a quick look. What university do you work at, out of curiosity? Sam On Oct 4, 2013, at 5:37 PM, Sung-Huan Yu <noreply(a)simtk.org> wrote: > You have been contacted by a member of Simtk.org. > > From: Sung-Huan Yu > Email: sunghuanyu(a)gmail.com > > The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff. > > > *** MESSAGE BEGINS *** > > Hi, > > Recently, I try to simulate RNA 3d structure from sequence. However, I usually get the results of strand crossing. I mean the one strand pierce through another strand ( it is very clear to see in New cartoon presentation). Therefore, they will aggregate together. Could you give me some suggestions to set some parameters to avoid this situation? I already try some parameters about atom steric. it will make the basepairings become wrong. I also tried some numbers of the baseInteractionScaleFactor. it still not works. Thank you

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MMB to quad-core computer
by Vasiliki E. Fadouloglou 26 Sep '13

26 Sep '13

Dear Dr Flores, I use MMB 2.13 in a quad-core computer (8GB RAM) and Ubuntu 13.04 64bit for folding an RNA. However, the job uses just one of the four available cores. I am wondering if I could share it to all four of them. Just one more question. There is the possibility to incorporate counterions and/or water in the calculations? Many thanks. Vasiliki ---------------------------------------------------------------- This message was sent using IMBB - WebMail.

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Re: MMB to quad-core computer
by Samuel Flores 25 Sep '13

25 Sep '13

kalispera Vasili, What forum did you post your question on? I would like to answer on there but I can't find it. To answer, MMB is currently still a single-processor code. You will unfortunately get no speedup from using a quad core machine. I can perhaps provide advice on how to speed up your calculation though. You will want to reduce degrees of freedom, and make sure you have no fast oscillations in your system that might force a small time step size. Let me know if you want help with this. Sam > Hello sam, > > The following is an e-mail sent to you by fadoulog via your account on > "Simtk.org Forums". If this message is spam, contains abusive or other > comments you find offensive please contact the webmaster of the board at > the following address: > > Simtk.org Forums <noreply(a)simtk.org> > > Include this full e-mail (particularly the headers). Please note that the > reply address to this e-mail has been set to that of fadoulog. > > Message sent to you follows > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dear Dr Flores, > > I use MMB 2.13 in a quad-core computer (8GB RAM) and Ubuntu 13.04 64bit for > folding an RNA. > However, the job uses just one of the four available cores. > I am wondering if I could share it to all four of them. > > Many thanks. > Vasiliki

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RNA threading problem
by UGUR UZAY Sezen 17 Sep '13

17 Sep '13

Dear MMBians, I am trying to thread around a section (nucleotides 57-91) of wheat 18S ribosomal RNA (3IZ7) using MMB_2.13. For some reason, instead of a hairpin I always get a straight helix. Strangely the target PDB file which is set rigid also becomes a linear molecule in the resulting PDB output. Can someone help me trouble shoot? I am attaching the command file, target pdb model and output pdb for you to see. Target pdb chain A: 3IZ7-57-91.pdb Command file threaded chain X: commands.3IZ7-threading-57-91.dat Result PDB: Sbi-16S-57-91 I appreciate your time and input, Uzay Sezen Uğur Uzay Sezen Post-Doctoral researcher Plant Genome Mapping Laboratory University of Georgia Center for Applied Genetic Technologies 111 Riverbend Rd., Athens, GA 30602 uzay(a)uga.edu<mailto:uzay@uga.edu> tel: 706-583-0170<tel:706-583-0170> fax: 706-583-8120<tel:706-583-8120> http://www.plantgenome.uga.edu/ http://naturedocumentaries.org/

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MMB 2.13 released
by Samuel Flores 13 Sep '13

13 Sep '13

Dear Users, I recommend upgrading to MMB 2.13. If you are using 2.12, you may encounter a bug with Physics where you want it, in which the bonded interactions are turned off. You may also note a speed improvement with 2.13. With regards, Sam

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