[gmx-users] Minimization Problem
Dear Gromacs community I am trying to run a simulation of choline molecule but found various errors concerning to bonds, angles and dihedrals during the minimization. Part of the top file (line number in the first column): ... 29 [ bonds ] 30; aiaj funct 311 4 1; N CT3 32114 1; N CT4 331 2 1; N CT1 341 3 1; N CT2 35212 1; CT1 HC12 36213 1; CT1 HC11 37211 1; CT1 HC13 383 7 1; CT2 HC21 393 6 1; CT2 HC22 403 5 1; CT2 HC23 414 8 1; CT3 HC31 42410 1; CT3 HC32 434 9 1; CT3 HC33 44 1417 1; CT4 HC41 45 1415 1; CT4 CT5 46 1416 1; CT4 HC42 47 1520 1; CT5 HC51 48 1518 1; CT5OH 49 1519 1; CT5 HC52 50 2118 1;HOOH ... Errors: ERROR 1 [file topol_choline.top, line 49]: No Default Bond type ERROR 2 [file topol_choline.top, line50]: No Default Bond type and so on with some of the angles and dihedrals... Does anybody have a clue on how to fix it? Thanks in advance. Ednilsom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ionic liquid simulation problem
Hi Ghosh, Thanks for your answer. But I'm not sure if I understood what you meant. I already used insert-molecules command to create a box with the cationic species. Now, should I use the same command to include the anionic species into the box? Best *Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola de Engenharia Industrial Metalúrgica de Volta Redonda* *Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa Cecília* *Volta Redonda**, Rio de Janeiro, Brasil* *CEP 27255-125* *Tel: +55-24-2107-3777* 2017-09-05 17:24 GMT-03:00 soumadwip ghosh: > Hi, > > I am not sure why you used the gmx solvate command for putting the > anionic species in your simulation box. It is meant for filling up the > simulation box with water molceules as the resname 'SOL' in the > topol.top file. Thus when you hit grompp it expects 'SOL' entry in > your topology file, cant find it and prints an error. In my opinion, > one should use the same gmx insert-molecules command for inserting the > anionic part into the box. If you dont want to use water in the > simulation you can proceed without the solvation step but cant use gmx > solvate for inserting anionic species or anything else. > > Best > Soumadwip Ghosh > Post Doctoral Research Associate > City of Hope Cancer Research Center > Duarte 91010 CA > USA > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Ionic liquid simulation problem.
*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola de Engenharia Industrial Metalúrgica de Volta Redonda* *Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa Cecília* *Volta Redonda**, Rio de Janeiro, Brasil* *CEP 27255-125* *Tel: +55-24-2107-3777* -- Forwarded message -- From: Ednilsom Orestes <eores...@gmail.com> Date: 2017-09-05 15:32 GMT-03:00 Subject: Ionic liquid simulation problem. To: gromacs.org_gmx-users@maillist.sys.kth.se Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the following protocol: 1. Prepared the respective PDB files and added/modified the OPLS/AA force field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp and ffnonbonded.itp files. 2. Used *pdb2gmx* command to create the respective .gro files, as well as, the posre.itp and topol.top files chossing OPLS/AA option without solvation. 3. Used the *insert-molecules* command to create a box filled with one specie (cation) and used the *solva**te* command to add the other specie (anion) as solvent into the same box. 4. Updated, by hand, the generated topol_box.top (pos_box.top) file including the topol.top and the posre.itp files of the other specie (anion) at the end of it. 5. I them tried to used the *grompp* command to minimize the energy of the cations+anions box and got the following error: Fatal error: Syntax error – File forcefield.itp, line 20 Last line read: ‘1 3yes 0.5 0.5' Found a second defaut directive. Does anyone knows whats is wrong with such a protocol? Thanks in advance. Ednilsom *Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola de Engenharia Industrial Metalúrgica de Volta Redonda* *Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa Cecília* *Volta Redonda**, Rio de Janeiro, Brasil* *CEP 27255-125* *Tel: +55-24-2107-3777 <+55%2024%202107-3777>* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Ionic liquid simulation problem.
Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the following protocol: 1. Prepared the respective PDB files and added/modified the OPLS/AA force field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp and ffnonbonded.itp files. 2. Used *pdb2gmx* command to create the respective .gro files, as well as, the posre.itp and topol.top files chossing OPLS/AA option without solvation. 3. Used the *insert-molecules* command to create a box filled with one specie (cation) and used the *solva**te* command to add the other specie (anion) as solvent into the same box. 4. Updated, by hand, the generated topol_box.top (pos_box.top) file including the topol.top and the posre.itp files of the other specie (anion) at the end of it. 5. I them tried to used the *grompp* command to minimize the energy of the cations+anions box and got the following error: Fatal error: Syntax error – File forcefield.itp, line 20 Last line read: ‘1 3yes 0.5 0.5' Found a second defaut directive. Does anyone knows whats is wrong with such a protocol? Thanks in advance. Ednilsom *Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola de Engenharia Industrial Metalúrgica de Volta Redonda* *Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa Cecília* *Volta Redonda**, Rio de Janeiro, Brasil* *CEP 27255-125* *Tel: +55-24-2107-3777* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.