Re: [gmx-users] Dihedral not counted?
Strange enough, those dihedrals are there, but the dihedral between atoms 2 9 10 and 17 is missing (in the main chain), altough defined in the PS residue (as -CH CH2 CH +CH2). I am still clueless... Greetings, Andrea 2008/10/27 Justin A. Lemkul <[EMAIL PROTECTED]>: > Well, there's no real problem, per se. Everything that you've given pdb2gmx > is in the topology; the issue is that you haven't specified any parameters > for those dihedrals: > > CH CB CG1 CG2 > CH CB CG5 CG4 > > 2 3 4 5 1 > 2 3 8 7 1 > > Makes sense that they'd be missing. If you're dealing with polystyrene, > maybe consider basing the dihedrals off of those contained in the PHE > sidechain in the Gromos force field you appear to be using. > > -Justin > > Andrea Muntean wrote: >> >> Here are the .rtp entries: >> >> >> [PS1] >> [atoms] >> CH3 CH3 0 0 >> CH CH1 0 0 >> CB C 0 0 >> CG1 CR1 0 0 >> CG2 CR1 0 0 >> CG3 CR1 0 0 >> CG4 CR1 0 0 >> CG5 CR1 0 0 >> >> [bonds] >> CH3 CH gb_26 >> CH CB gb_26 >> CB CG1 gb_15 >> CG1 CG2 gb_15 >> CG2 CG3 gb_15 >> CG3 CG4 gb_15 >> CG4 CG5 gb_15 >> CG5 CB gb_15 >> CH +CH2gb_26 >> >> [angles] >> ;109,5 angle >> CH3 CH +CH2ga_12 >> CH3 CH CB ga_12 >> CB CH +CH2ga_12 >> ;120 angle >> CH CB CG1 ga_26 >> CH CB CG5 ga_26 >> CG1 CB CG5 ga_26 >> CB CG1 CG2 ga_26 >> CG1 CG2 CG3 ga_26 >> CG2 CG3 CG4 ga_26 >> CG3 CG4 CG5 ga_26 >> CG4 CG5 CB ga_26 >> >> [impropers] >> ;keep the planarity of the ring >> CB CG1 CG2 CG3 gi_1 >> CG1 CG2 CG3 CG4 gi_1 >> CG2 CG3 CG4 CG5 gi_1 >> CG3 CG4 CG5 CB gi_1 >> CG4 CG5 CB CG1 gi_1 >> CG5 CB CG1 CG2 gi_1 >> ;around CB >> CB CG1 CG5 CH gi_1 >> CB CG5 CH CG1 gi_1 >> CB CH CG1 CG5 gi_1 >> ;around CH >> CH CB +CH2CH3 gi_1 >> CH +CH2CH3 CB gi_1 >> CH CH3 CB +CH2gi_1 >> >> [dihedrals] >> ;in the chain - 3-fold (n=3) >> CH3 CH +CH2+CH gd_16 >> CB CH +CH2+CH gd_16 >> ;around CH-CB - 2-fold (n=2) >> CH3 CH CB CG5 gd_1 >> CH3 CH CB CG1 gd_1 >> +CH2CH CB CG5 gd_1 >> +CH2CH CB CG1 gd_1 >> ;around CB-CG - 2-fold?,do we need them? >> CH CB CG1 CG2 >> CH CB CG5 CG4 >> >> >> [PS] >> [atoms] >> CH2 CH2 0 0 >> CH CH1 0 0 >> CB C 0 0 >> CG1 CR1 0 0 >> CG2 CR1 0 0 >> CG3 CR1 0 0 >> CG4 CR1 0 0 >> CG5 CR1 0 0 >> >> [bonds] >> -CH CH2 gb_26 >> CH2 CH gb_26 >> CH CB gb_26 >> CB CG1 gb_15 >> CG1 CG2 gb_15 >> CG2 CG3 gb_15 >> CG3 CG4 gb_15 >> CG4 CG5 gb_15 >> CG5 CB gb_15 >> CH +CH2gb_26 >> >> [angles] >> ;109,5 angle >> -CH CH2 CH ga_12 >> CH2 CH +CH2ga_12 >> CH2 CH CB ga_12 >> CB CH +CH2ga_12 >> ;120 angle >> CH CB CG1 ga_26 >> CH CB CG5 ga_26 >> CG1 CB CG5 ga_26 >> CB CG1 CG2 ga_26 >> CG1 CG2 CG3 ga_26 >> CG2 CG3 CG4 ga_26 >> CG3 CG4 CG5 ga_26 >> CG4 CG5 CB ga_26 >> >> [impropers] >> ;keep the planarity of the ring >> CB CG1 CG2 CG3 gi_1 >> CG1 CG2 CG3 CG4 gi_1 >> CG2 CG3 CG4 CG5 gi_1 >> CG3 CG4 CG5 CB gi_1 >> CG4 CG5 CB CG1 gi_1 >> CG5 CB CG1 CG2 gi_1 >> ;around CB >> CB CG1 CG5 CH gi_1 >> CB CG5 CH CG1 gi_1 >> CB CH CG1 CG5 gi_1 >> ;around CH >> CH CB +CH2CH2 gi_1 >> CH +CH2CH2 CB gi_1 >> CH CH2 CB +CH2gi_1 >> >> [dihedrals] >> ;in the chain - 3-fold >> CH2 CH +CH2+CH gd_16 >> CB CH +CH2+CH gd_16 >> -CH CH2 CH CB gd_16 >> -CH CH2 CH +CH2gd_16 >> ;around CH-CB - 2-fold >> CH2 CH CB CG5 gd_1 >> CH2 CH CB CG1 gd_1 >> +CH2CH CB CG5 gd_1 >> +CH2CH CB CG1 gd_1 >> ;around CB-CG - 2-fold?,do we need them? >> CH CB CG1 CG2 >> CH CB CG5 CG4 >> >> [ PSN ] >> [atoms] >> CH2 CH2 0 0 >> CH CH1 0 0 >> CB C 0 0 >> CG1 CR1 0 0 >> CG2 CR1 0 0 >> CG3 CR1 0 0 >> CG4 CR1 0 0 >
Re: [gmx-users] Dihedral not counted?
Sorry, once again for everybody in the list: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2 CH ga_12 CH2 CH CH3 ga_12 CH2 CH CB ga_12 CB CH CH3 ga_12 CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB CH3CH2 gi_1 CH CH3 CH2CB gi_1 CH CH2 CB CH3 gi_1 [dihedrals] ;in the chain - 3-fold (n=3) -CH CH2
Re: [gmx-users] Dihedral not counted?
Well, there's no real problem, per se. Everything that you've given pdb2gmx is in the topology; the issue is that you haven't specified any parameters for those dihedrals: CH CB CG1 CG2 CH CB CG5 CG4 2 3 4 5 1 2 3 8 7 1 Makes sense that they'd be missing. If you're dealing with polystyrene, maybe consider basing the dihedrals off of those contained in the PHE sidechain in the Gromos force field you appear to be using. -Justin Andrea Muntean wrote: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2 CH ga_12 CH2 CH CH3 ga_12 CH2 CH CB ga_12 CB CH CH3 ga_12 CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1
Re: [gmx-users] Dihedral not counted?
Andrea Muntean wrote: Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. Please send them as plain text to the list so everyone can see them without having to download the files (and so they can be archived for reference). -Justin For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the proper dihedrals, the impropers are OK). Thanks for your help. Andrea -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the proper dihedrals, the impropers are OK). Thanks for your help. Andrea RTP.pdf Description: Adobe PDF document TrimerTOP.pdf Description: Adobe PDF document ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Andrea Muntean wrote: Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals then I would expect. I did run the same for dimer and trimer. For dimer is ok, for trimer starts to count 1 dihedral less, and for the chain with 80 monomers corespondingly 78 dihedrals less, which means that the error should be in the inner residue. I checked many times, but the dihedral which is missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Without seeing the .rtp entry and the relevant portion of the resulting .top, it's hard to say. Can you post those pieces of information? -Justin Thanks in advance. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral not counted?
Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals then I would expect. I did run the same for dimer and trimer. For dimer is ok, for trimer starts to count 1 dihedral less, and for the chain with 80 monomers corespondingly 78 dihedrals less, which means that the error should be in the inner residue. I checked many times, but the dihedral which is missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Thanks in advance. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
