> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. OPLS implicit solvent problems (francesca.stanzi...@unina.it) > 2. Re: OPLS implicit solvent problems (Per Larsson) > 3. (no subject) (francesca.stanzi...@unina.it) > 4. CG to FG transformation error (Anirban Ghosh) > 5. Re: Problem with using topolbuild1_3.tgz (Bruce D. Ray) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Jan 2011 13:51:08 +0100 > From: francesca.stanzi...@unina.it > Subject: [gmx-users] OPLS implicit solvent problems > To: gmx-users@gromacs.org > Message-ID: <20110121135108.kg4c6rbjr44kg...@webmail.unina.it> > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello, > > I try to perform an implicit solvent simulation with Gromacs 4.5.3. > version. I have a system corresponding to 6 peptides generated by > Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA > and i put the N-and C- termini as NH2 and COOH. My topology file is > correct, and is all systems are included. > > ; Include forcefield parameters > #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is > included gbsa.itp > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #include "topol_Protein_chain_B.itp" > #include "topol_Protein_chain_C.itp" > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_E.itp" > #include "topol_Protein_chain_F.itp" > > ; Include water topology > #include "./oplsaa.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "./oplsaa.ff/ions.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_B 1 > Protein_chain_C 1 > Protein_chain_D 1 > Protein_chain_E 1 > Protein_chain_F 1 > ----------------------------------------------------------------------------- > > When I start my simulations (md_start.mdp) in implicit solvent, i > have this fatal error: > > GB parameter(s) missing or negative for atom type 'opls_912B' > > GB parameter(s) missing or negative for atom type 'opls_267' > > GB parameter(s) missing or negative for atom type 'opls_269' > > GB parameter(s) missing or negative for atom type 'opls_268' > > GB parameter(s) missing or negative for atom type 'opls_270' > > Program grompp, VERSION 4.5.3 > Source code file: grompp.c, line: 1123 > > Fatal error: > Can't do GB electrostatics; the implicit_genborn_params section of the > forcefield is missing parameters for 5 atomtypes or they might be > negative. > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors. > > > ---------------------------------------------------------------------------- > > Controlling these atoms they corresponding to: > > opls_912B= the CA of N-terminal residue > > opls_267= Co in COOH > > opls_268= Oh in COOH > > opls_269= Oc in COOH neutral > > opls_270= H in COOH > > ---------------------------------------- > > in the file gbsa.itp in opls.ff directory these atoms missing. Now, > have I done something wrong? If is all ok, is it possible to create > these missing atoms in the gbsa.itp file? > > thanx, > > francesca stanzione > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/10a6228e/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 21 Jan 2011 14:11:40 +0100 > From: Per Larsson <per.lars...@sbc.su.se> > Subject: Re: [gmx-users] OPLS implicit solvent problems > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <6ec741e6-55f1-41c0-b67a-bc133ab22...@sbc.su.se> > Content-Type: text/plain; charset="us-ascii" > > Hi! > > Thanks for pointing this out. > It is unfortunate that they are missing from the gbsa.itp-file. I will add > them, but I do not have time today. > If you want to get going, you can add them yourself. > The gb-parameters are essentially based on atom hybridization, so for each > missing atom you find another that has the same (sp, sp2,sp3) > hybridization, and add it to the gbsa.itp-file. > > Cheers > /Per > > 21 jan 2011 kl. 13.51 skrev francesca.stanzi...@unina.it: > >> Hello, >> >> I try to perform an implicit solvent simulation with Gromacs 4.5.3. >> version. I have a system corresponding to 6 peptides generated by Pymol >> with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put >> the N-and C- termini as NH2 and COOH. My topology file is correct, and >> is all systems are included. >> >> ; Include forcefield parameters >> #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is >> included gbsa.itp >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Protein_chain_B.itp" >> #include "topol_Protein_chain_C.itp" >> #include "topol_Protein_chain_D.itp" >> #include "topol_Protein_chain_E.itp" >> #include "topol_Protein_chain_F.itp" >> >> ; Include water topology >> #include "./oplsaa.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "./oplsaa.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Protein_chain_B 1 >> Protein_chain_C 1 >> Protein_chain_D 1 >> Protein_chain_E 1 >> Protein_chain_F 1 >> ----------------------------------------------------------------------------- >> >> When I start my simulations (md_start.mdp) in implicit solvent, i have >> this fatal error: >> >> GB parameter(s) missing or negative for atom type 'opls_912B' >> >> GB parameter(s) missing or negative for atom type 'opls_267' >> >> GB parameter(s) missing or negative for atom type 'opls_269' >> >> GB parameter(s) missing or negative for atom type 'opls_268' >> >> GB parameter(s) missing or negative for atom type 'opls_270' >> >> Program grompp, VERSION 4.5.3 >> Source code file: grompp.c, line: 1123 >> >> Fatal error: >> Can't do GB electrostatics; the implicit_genborn_params section of the >> forcefield is missing parameters for 5 atomtypes or they might be >> negative. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors. >> >> ---------------------------------------------------------------------------- >> >> Controlling these atoms they corresponding to: >> >> opls_912B= the CA of N-terminal residue >> >> opls_267= Co in COOH >> >> opls_268= Oh in COOH >> >> opls_269= Oc in COOH neutral >> >> opls_270= H in COOH >> >> ---------------------------------------- >> >> in the file gbsa.itp in opls.ff directory these atoms missing. Now, have >> I done something wrong? If is all ok, is it possible to create these >> missing atoms in the gbsa.itp file? >> >> thanx, >> >> francesca stanzione >> >> -- >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/cbbaa971/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Fri, 21 Jan 2011 14:44:17 +0100 > From: francesca.stanzi...@unina.it > Subject: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20110121144417.v2czlcmrbk8kk...@webmail.unina.it> > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Pers, > > thank you for reply. I'm trying to add these missing atoms with > your guideline, but I don't know if all parameters that I'm going to > add are corrects. When you have a time, can you add these missing > atoms in the program or can you help me to create a correct > substitution of these atoms? Because I can try to add the parameters > in the five coloumns present but I should know if these values are > right. > > thanks, > > francesca > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/8558f18f/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Fri, 21 Jan 2011 19:17:47 +0530 > From: Anirban Ghosh <reach.anirban.gh...@gmail.com> > Subject: [gmx-users] CG to FG transformation error > To: Discussion list for GROMACS users <gmx-users@gromacs.org>, Anirban > Ghosh <reach.anirban.gh...@gmail.com> > Message-ID: > <aanlktin9wesqmtv_lfo_4erqxodgpk6v802v85-3w...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am trying to convert a coarse grained protein to a full atom model after > CGMD. I am using the modified gromacs_reverse code available from MARTINI > site. I am using the following command: > > g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro > > But in the output full.gro all the atoms are having coordinate values as > "0.00". > > My pro_cg.top file looks like: > > #define _FF_GROMOS96 > #define _FF_GROMOS42A2 > ;#define _FF_GROMACS > ;#define _FF_GROMACS1 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 0.125 0.5 > > > #include "ffG43a2nb.itp" > #include "ffG43a2bon.itp" > > > Is this correct? where I am going wrong? I think the problem is with > pro_cg.top file only. > > Any suggestion is welcome. > > > Thanks, > > > -Anirban > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/30a6fbcc/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Fri, 21 Jan 2011 06:55:30 -0800 (PST) > From: "Bruce D. Ray" <bruced...@yahoo.com> > Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz > To: gmx-users@gromacs.org > Message-ID: <417950.70449...@web35801.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <i...@wehi.edu.au> wrote: >> Hi, I am trying to generate topology files for a set of lipids with the >> help of topolbuild1_3.tgz package found at the other software page of >> GROMACS website. >> >> I downloaded and installed all files and tried running the program with >> a >> MOL2 file with charges in it. However, it shows an error message as >> follows: >> >> Fatal error. >> Source code file: readmol2.c, line: 758 >> Atom 1 (C) has 3 connections when allowed 0 >> >> I am not sure how to get over this problem! Wonder what will fix this >> error and get the program running! > > A major requirement of topolbuild is that the mol2 file use correct atom > types as defined by Tripos, whose file format mol2 is, and as used in > Sybyl. > The error message suggests that you have not specified correct Tripos > Sybyl > atom types. There may be other problems in your mol2 file as well. > Correct the atom types and check that the file is otherwise syntactically > correct and it should work. > > However, I believe that lipid topology files for gromacs are already > available > for download. > > I hope that helps. > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273
Hi Bruce, Thanx for the reply. The MOL2 file was generated by the RESP ESP charge derive server. I did not check the file in SYBYL. However, structurally it seems correct. I will try reading it into sybyl and then resave it into another mol2 file. I am looking at making topology files for lipids like cardiolipin, di myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and myristoleic acid. DO you know of any available gromacs topology files for these? Cheers Sweta > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/bdd5ae9c/attachment.html > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 156 > ****************************************** > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
