From samuelfloresc at gmail.com Fri Sep 13 01:17:15 2013 From: samuelfloresc at gmail.com (Samuel Flores) Date: Fri Sep 13 01:17:22 2013 Subject: [RNABuilder-help] MMB 2.13 released Message-ID: <158C75D7-5B40-407A-B3BE-63CC15BB6ED0@gmail.com> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: https://simtk.org/pipermail/rnatoolbox-help/attachments/20130913/233aca9f/attachment.html From uzay at uga.edu Fri Sep 13 13:12:22 2013 From: uzay at uga.edu (UGUR UZAY Sezen) Date: Tue Sep 17 07:39:56 2013 Subject: [RNABuilder-help] RNA threading problem Message-ID: <7CEE28A2D055C84E8265BD5A8E81647D31702D29@BL2PRD0210MB386.namprd02.prod.outlook.com> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: 3Iz7-57-91.pdb Type: application/octet-stream Size: 43288 bytes Desc: 3Iz7-57-91.pdb Url : https://simtk.org/pipermail/rnatoolbox-help/attachments/20130913/67f1dea9/3Iz7-57-91-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: commands.3iz7-threading-57-91.dat Type: application/octet-stream Size: 1219 bytes Desc: commands.3iz7-threading-57-91.dat Url : https://simtk.org/pipermail/rnatoolbox-help/attachments/20130913/67f1dea9/commands.3iz7-threading-57-91-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Sbi-16S-57-91.pdb Type: application/octet-stream Size: 366835 bytes Desc: Sbi-16S-57-91.pdb Url : https://simtk.org/pipermail/rnatoolbox-help/attachments/20130913/67f1dea9/Sbi-16S-57-91-0001.obj From samuelfloresc at gmail.com Tue Sep 17 08:16:46 2013 From: samuelfloresc at gmail.com (Samuel Flores) Date: Tue Sep 17 08:16:55 2013 Subject: [RNABuilder-help] RNA threading problem In-Reply-To: <7CEE28A2D055C84E8265BD5A8E81647D31702D29@BL2PRD0210MB386.namprd02.prod.outlook.com> References: <7CEE28A2D055C84E8265BD5A8E81647D31702D29@BL2PRD0210MB386.namprd02.prod.outlook.com> Message-ID: <06665BAC-AA7B-4B9C-8229-B11E15D097C6@gmail.com> Sorry your message was stuck waiting for approval because of the attachment size. I've now increased the limit to 1000 kB. I think I have solved about 80% of your problem. Since several residues were represented only by their "P" atoms, MMB was probably not able to match structure. I have deleted these incomplete residues. I also added a model of chain "X" as an extended chain (I can do this by doing a stage 1 MMB run). I then used "loadSequencesFromPdb," which reads sequences and residue numbers directly from last.1.pdb, and tolerates missing residues (as long as the remaining residues have all their backbone atoms). I adjusted the "threading" command to not thread the missing residues. I fixed chain A to the Ground frame (rootMobilizer A Weld). Lastly, I turned on the Amber99 potential for chain X only (with setDefaultMDParameters and "includeAllNonBondAtomsInResidues X 57 91"). So now, the only part not threaded is the span from residue 71 to 81. If you want to thread to the "P" atoms from those residues in chain A, I suggest creating eleven "springToGround" commands, connecting the P atoms on chain X to the locations of the P atoms on chain X. Look at the reference guide for the springToGround syntax. You may want a nice strong spring constant, e.g. 300 or more. Let me know how you do with the last part. I have attached my commands.dat and last.1.pdb. Sam > 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 > > U?ur Uzay Sezen > Post-Doctoral researcher > Plant Genome Mapping Laboratory > University of Georgia > Center for Applied Genetic Technologies > 111 Riverbend Rd., Athens, GA 30602 > uzay@uga.edu > tel: 706-583-0170 > fax: 706-583-8120 > http://www.plantgenome.uga.edu/ > http://naturedocumentaries.org/ > <3Iz7-57-91.pdb>_______________________________________________ > Rnatoolbox-help mailing list > Rnatoolbox-help@simtk.org > https://simtk.org/mailman/listinfo/rnatoolbox-help -------------- next part -------------- Skipped content of type multipart/mixed From samuelfloresc at gmail.com Wed Sep 25 07:30:24 2013 From: samuelfloresc at gmail.com (Samuel Flores) Date: Wed Sep 25 07:30:25 2013 Subject: [RNABuilder-help] Re: MMB to quad-core computer In-Reply-To: <82e55619c395aa047ba716467cccacc9@simtk.org> References: <82e55619c395aa047ba716467cccacc9@simtk.org> Message-ID: <84EBCC19-1447-479D-9DD5-57058FE34CB1@gmail.com> 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 > > 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 From fadoulog at imbb.forth.gr Wed Sep 25 22:47:19 2013 From: fadoulog at imbb.forth.gr (Vasiliki E. Fadouloglou) Date: Wed Sep 25 22:47:41 2013 Subject: [RNABuilder-help] MMB to quad-core computer Message-ID: <20130926084719.ao4j37cxzc4kg0ok@webmail2.imbb.forth.gr> 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. From samuel.flores at icm.uu.se Thu Sep 26 01:22:30 2013 From: samuel.flores at icm.uu.se (Samuel Coulbourn Flores) Date: Thu Sep 26 01:22:34 2013 Subject: [RNABuilder-help] MMB to quad-core computer In-Reply-To: <20130926084719.ao4j37cxzc4kg0ok@webmail2.imbb.forth.gr> References: <20130926084719.ao4j37cxzc4kg0ok@webmail2.imbb.forth.gr> Message-ID: Hi Vasiliki, > > Dear Sam, > > I used your email from the 'Public Forum' in this link: > https://simtk.org/forums/memberlist.php?mode=email&u=482 > > It would be very useful if I could speedup the calculations as my system is a big one (it is a 180nt RNA). I will go back to my protocol (.dat) and trying to find out which keywords control degrees of freedom and oscillations. > See whether you can reduce the flexibility by rigidifying parts of your system that don't need to move.. use "mobilizer Rigid". Maybe solve one piece of the system at a time, changing the flexible zone accordingly. Look for any large forces that would create sharp jumps at the first reporting interval. If the simulation progresses too slowly, you can set reportingInterval very small, just so you can see what is happening. > Just one more question. There is the possibility to incorporate counterions and/or water in the calculations? > You can use the monoAtoms and waterDroplet commands. They are in the reference guide. However there are a few caveats: 1. monoAtoms in 2.13 can instantiate the ions, but not turn on their PARM99 force field terms using "Physics where you want it." You may be able to turn them on if all molecules in your system have the force field terms turned on. In 2.14 this is corrected, but 2.14 has not been released yet, you would have to compile, or if you're on Mac I could send you a pre-release compiled version. 2. You have to be careful about atom names, chain ID, and residue type in your input pdb, in order to read in the ion coordiantes from a file. For instance, for Magnesium the atom name is "Mg+2", the residue type is "MG", and the chain ID has to be different from that of any biopolymers in your system. 3. water molecule positions cannot be read from a PDB file. You would create a new water droplet every time you run. 4. Most importantly, we haven't properly benchmarked water and ion performance. There are some problems with water -- I've seen close contacts between water and biopolymer kick a backbone through a proline cycle, for instance. So you're welcome to use it, but at the moment I would not compare the results to those you would get from MD. Thanks Sam > Many thanks > Vasiliki > > > Quoting Samuel Flores : > >> >> 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 >>> >>> 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 >> >> > > > > -- > Vasiliki E. Fadouloglou, PhD > Marie Curie Fellow > IMBB/Forth and Democritus University of Thrace > Tel +306973969995 > email fadoulog@imbb.forth.gr, fadoulog@mbg.duth.gr > > ---------------------------------------------------------------- > This message was sent using IMBB - WebMail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://simtk.org/pipermail/rnatoolbox-help/attachments/20130926/ad5ddc6c/attachment.html