[gmx-users] Strange error in DNA simulations..
Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are.. pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. For this experiment, here is the error report which I donot understand at all! The error report is really frightening to me!!! Here it is! [bh...@localhost doublestrand]$ gedit Testfile [bh...@localhost doublestrand]$ mpirun N C Testfile NNODES=2, MYRANK=1, HOSTNAME=localhost.localdomain NNODES=2, MYRANK=0, HOSTNAME=localhost.localdomain NODEID=1 argc=6 NODEID=0 argc=6 :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.0.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun_d (double precision) (-: Option Filename Type Description -s bhanu.tpr InputRun input file: tpr tpb tpa -o bhanu.trr Output Full precision trajectory: trr trj cpt -x bhanu.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi bhanu.cpt Input, Opt. Checkpoint file -cpo bhanu.cpt Output, Opt. Checkpoint file -c bhanu.gro Output Structure file: gro g96 pdb -e bhanu.edr Output Energy file: edr ene -g bhanu.log Output Log file -dgdl bhanu.xvg Output, Opt. xvgr/xmgr file -fieldbhanu.xvg Output, Opt. xvgr/xmgr file -tablebhanu.xvg Input, Opt. xvgr/xmgr file -tablep bhanu.xvg Input, Opt. xvgr/xmgr file -tableb bhanu.xvg Input, Opt. xvgr/xmgr file -rerunbhanu.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi bhanu.xvg Output, Opt. xvgr/xmgr file -tpid bhanu.xvg Output, Opt. xvgr/xmgr file -ei bhanu.edi Input, Opt. ED sampling input -eo bhanu.edo Output, Opt. ED sampling output -j bhanu.gct Input, Opt. General coupling stuff -jo bhanu.gct Output, Opt. General coupling stuff -ffoutbhanu.xvg Output, Opt. xvgr/xmgr file -devout bhanu.xvg Output, Opt. xvgr/xmgr file -runavbhanu.xvg Output, Opt. xvgr/xmgr file -px bhanu.xvg Output, Opt. xvgr/xmgr file -pf bhanu.xvg Output, Opt. xvgr/xmgr file -mtx bhanu.mtx Output, Opt. Hessian matrix -dn bhanu.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string bhanu Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool yes Sum the energies at every step -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each
Re: [gmx-users] Strange error in DNA simulations..
On 06/15/09, Bhanu bhanui...@gmail.com wrote: Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are.. pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. So look up how to configure LAM-MPI to use more. For this experiment, here is the error report which I donot understand at all! The error report is really frightening to me!!! Here it is! See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange error in DNA simulations..
On 15/06/2009, Mark Abraham mark.abra...@anu.edu.au wrote: On 06/15/09, *Bhanu *bhanui...@gmail.com wrote: Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are.. pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. So look up how to configure LAM-MPI to use more. I am working on that.. but the real confusing thing, is why are DNA simulations failing?? I have no clue.. and requesting for a suggestion! For this experiment, here is the error report which I donot understand at all! The error report is really frightening to me!!! Here it is! See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange error in DNA simulations..
Hi, I didn't ignore your link, I was trying all things suggested in wiki.. Its the greed for more and more suggestions made me to type those.. Anyway, thanks for the link, buddy! On 15/06/2009, Mark Abraham mark.abra...@anu.edu.au wrote: On 06/15/09, *Bhanu *bhanui...@gmail.com wrote: On 15/06/2009, Mark Abraham mark.abra...@anu.edu.au wrote: On 06/15/09, *Bhanu *bhanui...@gmail.com wrote: Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are.. pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. So look up how to configure LAM-MPI to use more. I am working on that.. but the real confusing thing, is why are DNA simulations failing?? I have no clue.. and requesting for a suggestion! I gave you a link to content that was likely to explain why your problem was occurring. If you appear to ignore it, then you won't be likely to get more :-) Mark For this experiment, here is the error report which I donot understand at all! The error report is really frightening to me!!! Here it is! See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulation Temperature for GPCR in POPC bilayer
Hi ALL, Thanks a lot for your replies regarding extending water box. I could finally solve the problem by first removing the periodicity from the original POPC pdb files and then properly using editconf with -box option. In Justin's tutorial on setting up a membrane simulation, the temperature used is 323K (reason is that temperature should be above phase transition temp ) which has been used in many papers as well. My question: is 323K ok for the embedded protein also?Does'nt it affect its stability? And, is 323K applicable for POPC as well? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation Temperature for GPCR in POPC bilayer
Anirban Ghosh wrote: Hi ALL, Thanks a lot for your replies regarding extending water box. I could finally solve the problem by first removing the periodicity from the original POPC pdb files and then properly using editconf with -box option. In Justin's tutorial on setting up a membrane simulation, the temperature used is 323K (reason is that temperature should be above phase transition temp ) which has been used in many papers as well. My question: is 323K ok for the embedded protein also?Does'nt it affect its stability? And, is 323K applicable for POPC as well? Any suggestion is welcome. Thanks a lot in advance. I recently updated the site with some suggestions for such temperatures. There is no substitute, however, for reading the literature (both experimental and theoretical) to understand what others are doing and why they are doing it. -Justin Regards, *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] prodrg 4.5beta generated topologies and exclusions
Dean Cue bas wrote: Hello all. Just a quick clarification, please. Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3) interactions are always excluded, and that third neighbor (1-4) non-bonding interactions are used, yet modified in some circumstances. The paper also states that all (1-4) interactions should be explicitly excluded for atoms either within or directly bonded to aromatic rings to help keep planarity. I could confirm this in the adenine topology in the ffG53a6.rtp file where there were the above described exclusions in the [exclusions] section for that residue. Now my questions. Prodrg4.5beta produces .itp files for all my ligands where under the [moleculetype] section it states that nrexcl is 3. Doesn’t this automatically exclude all (1-4) interactions for that ligand? Yes, such interactions are excluded. If so, then doesn’t that automatically negate the need to explicitly exclude the (1-4) interactions for planar aromatic systems as described above in the ff paper? The authors of that paper were probably not pre-supposing the use of any particular topology-generation tool. If so, then doesn’t excluding all these third neighbor (1-4) interactions for ligand topologies produced by Prodrg ignore intra-molecular interactions that are important in the simulated behavior and properties of these ligands? It would seem so. If this bothered me, I would start by reading the PRODRG documentation - but I would have done that before using anything it generated. Doesn’t this imply that the default for ffG53a6 intra-molecular protein-atom/protein-atom non-bonded interactions is nrexcl =2 ? That might depend on the mechanism that is being used for the different and/or missing 1-4 interactions. Pre-excluding and then adding might be easier than pre-including and then excluding. Thanks in advance for any clarification in this area. I just want to be sure I’m accounting for my exclusions properly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -ighn failing with ffamber
Alan wrote: Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh I am getting: WARNING: atom H is missing in residue GLY 2 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing --- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] Namber99_34 -0.41570 1 Hamber99_17 0.27190 2 CAamber99_11 -0.02520 3 HA1amber99_19 0.06980 4 HA2amber99_19 0.06980 5 Camber99_20.59730 6 Oamber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only atom H is missing in residue GLY 2. If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding a negative two charged ion
CandyCandy wrote: Dear gromacs users, I am using genion command to add a negative two charged ion: genion -s water.tpr -o watern.gro -nq 2 -nname O- -nn 1 -g watern.log. Well, -nq 2 will set a charge of +2, not -2. It does not work. It shows: Fatal error: No such moleculetype O Could anybody give me some idea about making a -2 charged ion? Thank you so much! Probably because such a species does not exist within the force field you're trying to use. Check out ions.itp for existing ion types. If you have to create a new species, you have the very difficult task of parameterization ahead of you: http://oldwiki.gromacs.org/index.php/Parameterization -Justin Best regards, Candy 立刻下载 MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ http://im.live.cn/safe/ ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] adding a negative two charged ion
Dear gromacs users, I am using genion command to add a negative two charged ion: genion -s water.tpr -o watern.gro -nq 2 -nname O- -nn 1 -g watern.log. It does not work. It shows: Fatal error: No such moleculetype O Could anybody give me some idea about making a -2 charged ion? Thank you so much! Best regards, Candy _ Messenger10年嘉年华，礼品大奖等你拿！ http://10.msn.com.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help with the topology file
hi gmx users I´m an undergraduate student of bachelor degree in chemistry at Distrital University in Bogota Colombia. I´m doing my thesis in polymers and learning how to use gromacs, moreover I have seen your lecture about gromacs but I have a problem, I do not know how to make the topology file to my polymer, so if you could help me how to make the topology file I would be grateful. *Yours Sincerely,* Danilo Gonzalez Universidad Distrital Francisco Jose de Caldas Bogota, colombia ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: -ighn failing with ffamber
Thank you Justin, You noticed well that. But this example was built to work without -ignh and to exemplify my problem, because in real case I have this protein and either I can use 'sed' to fix it (mainly H names) I found it annoying sometimes, so why not -ignh? Cheers, Alan On Mon, Jun 15, 2009 at 15:51, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh I am getting: WARNING: atom H is missing in residue GLY 2 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing --- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] N amber99_34 -0.41570 1 H amber99_17 0.27190 2 CA amber99_11 -0.02520 3 HA1 amber99_19 0.06980 4 HA2 amber99_19 0.06980 5 C amber99_2 0.59730 6 O amber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only atom H is missing in residue GLY 2. If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Making a .pdb file that actually works?
I've tried multiple times to make a pdb file that will work with pdb2gmx. I've even drawn the molecule into PRODRG but the structure will still not work. I simply want a poly(benzyl-L-glutamate) with 5 repeat units. How in the world can I get this to work? Thank you for your time. _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making a .pdb file that actually works?
Joseph Johnson wrote: I've tried multiple times to make a pdb file that will work with pdb2gmx. I've even drawn the molecule into PRODRG but the structure will still not work. I simply want a poly(benzyl-L-glutamate) with 5 repeat units. How in the world can I get this to work? If it is a repeat unit then you can define the constituent building blocks within the corresponding .rtp file. The PDB file is not likely the problem, but if you want more useful help, you'll have to describe the difficulty you're having fully, including real error messages and snippets of the relevant structure and .rtp entries. -Justin Thank you for your time. Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: -ighn failing with ffamber
Alan wrote: Thank you Justin, You noticed well that. But this example was built to work without -ignh and to exemplify my problem, because in real case I have this protein and either I can use 'sed' to fix it (mainly H names) I found it annoying sometimes, so why not -ignh? No idea. I can successfully process your .pdb file with and without -ignh, and I get the same result (a correct topology) each time. Have you run the test suite to validate your installation? Maybe if you post the details of your hardware, compilers, OS, etc. someone can spot something that might be problematic (i.e., a bug). -Justin Cheers, Alan On Mon, Jun 15, 2009 at 15:51, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh I am getting: WARNING: atom H is missing in residue GLY 2 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing --- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] Namber99_34 -0.41570 1 Hamber99_17 0.27190 2 CAamber99_11 -0.02520 3 HA1amber99_19 0.06980 4 HA2amber99_19 0.06980 5 Camber99_20.59730 6 Oamber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only atom H is missing in residue GLY 2. If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: -ighn failing with ffamber
Hi Justin, Please, confirm this, you mean that this pdb worked for you with '-ignh'? Gosh... So I may not loosing my mind when I said that it was working before. So, I am running: - Mac Osx 10.5.7 intel. - Gromacs 4.0.5 (from Fink) with ffamber; - Compilers from Fink. I ran test suite and although I got some fails for complex and kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite would fail because oplsaa is working fine here if I do 'pdb2gmx -f GGG.pdb -ff oplsaa -ignh' In any case, many thanks for your attention Justin, Alan On Mon, Jun 15, 2009 at 20:01, gmx-users-requ...@gromacs.org wrote: Alan wrote: Thank you Justin, You noticed well that. But this example was built to work without -ignh and to exemplify my problem, because in real case I have this protein and either I can use 'sed' to fix it (mainly H names) I found it annoying sometimes, so why not -ignh? No idea. I can successfully process your .pdb file with and without -ignh, and I get the same result (a correct topology) each time. Have you run the test suite to validate your installation? Maybe if you post the details of your hardware, compilers, OS, etc. someone can spot something that might be problematic (i.e., a bug). -Justin Cheers, Alan On Mon, Jun 15, 2009 at 15:51, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh I am getting: WARNING: atom H is missing in residue GLY 2 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing --- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] N amber99_34 -0.41570 1 H amber99_17 0.27190 2 CA amber99_11 -0.02520 3 HA1 amber99_19 0.06980 4 HA2 amber99_19 0.06980 5 C amber99_2 0.59730 6 O amber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only atom H is missing in residue GLY 2. If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search
Re: [gmx-users] Re: -ighn failing with ffamber
Alan wrote: Hi Justin, Please, confirm this, you mean that this pdb worked for you with '-ignh'? Gosh... Correct. So I may not loosing my mind when I said that it was working before. So, I am running: - Mac Osx 10.5.7 intel. - Gromacs 4.0.5 (from Fink) with ffamber; - Compilers from Fink. Identical to my system, except I compiled from source. Perhaps the fink package is broken? -Justin I ran test suite and although I got some fails for complex and kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite would fail because oplsaa is working fine here if I do 'pdb2gmx -f GGG.pdb -ff oplsaa -ignh' In any case, many thanks for your attention Justin, Alan On Mon, Jun 15, 2009 at 20:01, gmx-users-requ...@gromacs.org wrote: Alan wrote: Thank you Justin, You noticed well that. But this example was built to work without -ignh and to exemplify my problem, because in real case I have this protein and either I can use 'sed' to fix it (mainly H names) I found it annoying sometimes, so why not -ignh? No idea. I can successfully process your .pdb file with and without -ignh, and I get the same result (a correct topology) each time. Have you run the test suite to validate your installation? Maybe if you post the details of your hardware, compilers, OS, etc. someone can spot something that might be problematic (i.e., a bug). -Justin Cheers, Alan On Mon, Jun 15, 2009 at 15:51, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh I am getting: WARNING: atom H is missing in residue GLY 2 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing --- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] Namber99_34 -0.41570 1 Hamber99_17 0.27190 2 CAamber99_11 -0.02520 3 HA1amber99_19 0.06980 4 HA2amber99_19 0.06980 5 Camber99_20.59730 6 Oamber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only atom H is missing in residue GLY 2. If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[gmx-users] B3LYP/6-31++G** GAMESS derived charges to replace PRODRG assigned ones
Dear all... Can I replace the charges that I get from B3LYP/6-31++G** GAMESS derived with the original PRODRG charges? Is this the right way to proceed ? Thanks.. IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] B3LYP/6-31++G** GAMESS derived charges to replace PRODRG assigned ones
naimah haron naimah wrote: Dear all... Can I replace the charges that I get from B3LYP/6-31++G** GAMESS derived with the original PRODRG charges? Is this the right way to proceed ? Quantum calculations are not necessary for Gromos parameterization. Refer to the primary literature for your parameter set of interest. -Justin Thanks.. IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb does not work.
Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command: pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro and I tell it to do: 0: GROMOS96 43a1 force field The output I get is: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue '1' not found in residue topology database Why is it giving me this output? Here is my pdb file and thank you for your help :) HETATM1 C 1 -3.361 1.127 2.911 C HETATM2 H 1 0.919 3.113 3.939 H HETATM3 H 1 -0.857 0.007 3.031 H HETATM4 H 1 -3.184 0.097 4.698 H HETATM5 H 1 -5.242 0.080 2.911 H HETATM6 O 1 -4.328 0.360 0.373 O HETATM7 H 1 -5.934 2.635 1.818 H HETATM8 H 1 -6.637 2.054 -0.750 H HETATM9 H 1 -4.459 1.860 -2.600 H HETATM 10 H 1 -5.242 -0.129 -4.291 H HETATM 11 C 1 -5.524 2.053 -0.750 C HETATM 12 H 1 -4.698 -2.790 -3.382 H HETATM 13 H 1 -6.834 -4.217 -4.291 H HETATM 14 H 1 -9.153 -2.809 -3.382 H HETATM 15 H 1 -9.153 -4.576 -3.382 H HETATM 16 H 1 -3.758 -0.655 -3.381 H HETATM 17 O 1 -1.506 2.874 3.937 O HETATM 18 O 1 0.594 2.197 3.939 O HETATM 19 H 1 -0.858 0.009 4.849 H HETATM 20 C 1 -0.722 1.955 3.939 C HETATM 21 N 1 -5.355 -2.021 -3.382 N HETATM 22 C 1 -1.227 0.533 3.939 C HETATM 23 N 1 -2.677 0.534 3.939 N HETATM 24 O 1 -2.756 1.649 2.005 O HETATM 25 H 1 -5.240 1.655 3.818 H HETATM 26 C 1 -4.870 1.129 2.910 C HETATM 27 N 1 -5.352 1.811 1.725 N HETATM 28 H 1 -5.152 3.102 -0.751 H HETATM 29 C 1 -5.022 1.342 0.483 C HETATM 30 N 1 -5.042 1.369 -1.934 N HETATM 31 O 1 -6.068 -0.528 -1.354 O HETATM 32 C 1 -5.373 0.058 -2.150 C HETATM 33 C 1 -4.871 -0.654 -3.382 C HETATM 34 O 1 -7.486 -1.352 -3.382 O HETATM 35 H 1 -6.834 -4.217 -2.473 H HETATM 36 C 1 -7.205 -3.693 -3.382 C HETATM 37 N 1 -8.643 -3.693 -3.382 N HETATM 38 C 1 -6.701 -2.270 -3.382 C CONECT1 24 23 26 CONECT2 18 CONECT3 22 CONECT4 23 CONECT5 26 CONECT6 29 CONECT7 27 CONECT8 11 CONECT9 30 CONECT 10 33 CONECT 118 28 29 30 CONECT 12 21 CONECT 13 36 CONECT 14 37 CONECT 15 37 CONECT 16 33 CONECT 17 20 CONECT 182 20 CONECT 19 22 CONECT 20 17 18 22 CONECT 21 12 33 38 CONECT 223 19 20 23 CONECT 234 221 CONECT 241 CONECT 25 26 CONECT 265 251 27 CONECT 277 26 29 CONECT 28 11 CONECT 296 27 11 CONECT 309 11 32 CONECT 31 32 CONECT 32 31 30 33 CONECT 33 10 16 32 21 CONECT 34 38 CONECT 35 36 CONECT 36 13 37 38 35 CONECT 37 14 15 36 CONECT 38 34 21 36 END _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pdb does not work.
Because pdb2gmx has to know what residue(s) are contained in the .pdb file, and the third column identifies the residue and as the program has told you, it is called 1. And it does not have a 1 residue on the .rtp file associated with that forcefield. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb does not work.
Joseph Johnson wrote: Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command: pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro and I tell it to do: 0: GROMOS96 43a1 force field The output I get is: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue '1' not found in residue topology database Why is it giving me this output? Here is my pdb file and thank you for your help :) ... because your PDB file does not name your residues. pdb2gmx isn't magic - it depends on the residue name to recognize which entry in the residue topology database (.rtp file) should be applied. So, read the PDB format document to work out which columns should have GLY, or use a known-good PDB file to copy the right columns. Mark HETATM1 C 1 -3.361 1.127 2.911 C HETATM2 H 1 0.919 3.113 3.939 H HETATM3 H 1 -0.857 0.007 3.031 H HETATM4 H 1 -3.184 0.097 4.698 H HETATM5 H 1 -5.242 0.080 2.911 H HETATM6 O 1 -4.328 0.360 0.373 O HETATM7 H 1 -5.934 2.635 1.818 H HETATM8 H 1 -6.637 2.054 -0.750 H HETATM9 H 1 -4.459 1.860 -2.600 H HETATM 10 H 1 -5.242 -0.129 -4.291 H HETATM 11 C 1 -5.524 2.053 -0.750 C HETATM 12 H 1 -4.698 -2.790 -3.382 H HETATM 13 H 1 -6.834 -4.217 -4.291 H HETATM 14 H 1 -9.153 -2.809 -3.382 H HETATM 15 H 1 -9.153 -4.576 -3.382 H HETATM 16 H 1 -3.758 -0.655 -3.381 H HETATM 17 O 1 -1.506 2.874 3.937 O HETATM 18 O 1 0.594 2.197 3.939 O HETATM 19 H 1 -0.858 0.009 4.849 H HETATM 20 C 1 -0.722 1.955 3.939 C HETATM 21 N 1 -5.355 -2.021 -3.382 N HETATM 22 C 1 -1.227 0.533 3.939 C HETATM 23 N 1 -2.677 0.534 3.939 N HETATM 24 O 1 -2.756 1.649 2.005 O HETATM 25 H 1 -5.240 1.655 3.818 H HETATM 26 C 1 -4.870 1.129 2.910 C HETATM 27 N 1 -5.352 1.811 1.725 N HETATM 28 H 1 -5.152 3.102 -0.751 H HETATM 29 C 1 -5.022 1.342 0.483 C HETATM 30 N 1 -5.042 1.369 -1.934 N HETATM 31 O 1 -6.068 -0.528 -1.354 O HETATM 32 C 1 -5.373 0.058 -2.150 C HETATM 33 C 1 -4.871 -0.654 -3.382 C HETATM 34 O 1 -7.486 -1.352 -3.382 O HETATM 35 H 1 -6.834 -4.217 -2.473 H HETATM 36 C 1 -7.205 -3.693 -3.382 C HETATM 37 N 1 -8.643 -3.693 -3.382 N HETATM 38 C 1 -6.701 -2.270 -3.382 C CONECT1 24 23 26 CONECT2 18 CONECT3 22 CONECT4 23 CONECT5 26 CONECT6 29 CONECT7 27 CONECT8 11 CONECT9 30 CONECT 10 33 CONECT 118 28 29 30 CONECT 12 21 CONECT 13 36 CONECT 14 37 CONECT 15 37 CONECT 16 33 CONECT 17 20 CONECT 182 20 CONECT 19 22 CONECT 20 17 18 22 CONECT 21 12 33 38 CONECT 223 19 20 23 CONECT 234 221 CONECT 241 CONECT 25 26 CONECT 265 251 27 CONECT 277 26 29 CONECT 28 11 CONECT 296 27 11 CONECT 309 11 32 CONECT 31 32 CONECT 32 31 30 33 CONECT 33 10 16 32 21 CONECT 34 38 CONECT 35 36 CONECT 36 13 37 38 35 CONECT 37 14 15 36 CONECT 38 34 21 36 END Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290
[gmx-users] replacing PRODRG charges with GAMESS charges
Dear all... I want to run a MD in an unparameterized molecule ionics liquids. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with gamess software? The target forcefield will be OPLS. Thanks... IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] replacing PRODRG charges with GAMESS charges
naimah haron naimah wrote: Dear all... I want to run a MD in an unparameterized molecule ionics liquids. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with gamess software? The target forcefield will be OPLS. This question has been answered twice in the last two days. PRODRG is not a tool for use with the OPLS force fields. Read the primary literature for your force field of interest. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
