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 +CH2 gb_26 >> >> [angles] >> ;109,5 angle >> CH3 CH +CH2 ga_12 >> CH3 CH CB ga_12 >> CB CH +CH2 ga_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 +CH2 CH3 gi_1 >> CH +CH2 CH3 CB gi_1 >> CH CH3 CB +CH2 gi_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 >> +CH2 CH CB CG5 gd_1 >> +CH2 CH 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 +CH2 gb_26 >> >> [angles] >> ;109,5 angle >> -CH CH2 CH ga_12 >> CH2 CH +CH2 ga_12 >> CH2 CH CB ga_12 >> CB CH +CH2 ga_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 +CH2 CH2 gi_1 >> CH +CH2 CH2 CB gi_1 >> CH CH2 CB +CH2 gi_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 +CH2 gd_16 >> ;around CH-CB - 2-fold >> CH2 CH CB CG5 gd_1 >> CH2 CH CB CG1 gd_1 >> +CH2 CH CB CG5 gd_1 >> +CH2 CH 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 CH3 CH2 gi_1 >> CH CH3 CH2 CB gi_1 >> CH CH2 CB CH3 gi_1 >> >> [dihedrals] >> ;in the chain - 3-fold (n=3) >> -CH CH2 CH CB gd_16 >> -CH CH2 CH CH3 gd_16 >> ;around CH-CB - 2-fold (n=2) >> CH2 CH CB CG5 gd_1 >> CH2 CH CB CG1 gd_1 >> CH3 CH CB CG5 gd_1 >> CH3 CH CB CG1 gd_1 >> ;around CB-CG - 2-fold?,do we need them? >> CH CB CG1 CG2 >> CH CB CG5 CG4 >> CB CG1 CG5 CH gi_1 >> CB CG5 CH CG1 gi_1 >> CB CH CG1 CG5 gi_1 >> ;around CH >> CH CB CH3 CH2 gi_1 >> CH CH3 CH2 CB gi_1 >> CH CH2 CB CH3 gi_1 >> >> [dihedrals] >> ;in the chain - 3-fold (n=3) >> -CH CH2 CH CB gd_16 >> -CH CH2 CH CH3 gd_16 >> ;around CH-CB - 2-fold (n=2) >> CH2 CH CB CG5 gd_1 >> CH2 CH CB CG1 gd_1 >> CH3 CH CB CG5 gd_1 >> CH3 CH CB CG1 gd_1 >> ;around CB-CG - 2-fold?,do we need them? >> CH CB CG1 CG2 >> CH CB CG5 CG4 >> >> >> And the .top file for the trimer, only the [atoms] and [dihedrals] >> (only the proper dihedrals) part: >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass >> typeB chargeB massB >> 1 CH3 1 PS1 CH3 1 0 15.035 ; >> qtot 0 >> 2 CH1 1 PS1 CH 1 0 13.019 ; >> qtot 0 >> 3 C 1 PS1 CB 1 0 12.011 ; >> qtot 0 >> 4 CR1 1 PS1 CG1 1 0 13.019 ; >> qtot 0 >> 5 CR1 1 PS1 CG2 1 0 13.019 ; >> qtot 0 >> 6 CR1 1 PS1 CG3 1 0 13.019 ; >> qtot 0 >> 7 CR1 1 PS1 CG4 1 0 13.019 ; >> qtot 0 >> 8 CR1 1 PS1 CG5 1 0 13.019 ; >> qtot 0 >> 9 CH2 2 PS CH2 2 0 14.027 ; >> qtot 0 >> 10 CH1 2 PS CH 2 0 13.019 ; >> qtot 0 >> 11 C 2 PS CB 2 0 12.011 ; >> qtot 0 >> 12 CR1 2 PS CG1 2 0 13.019 ; >> qtot 0 >> 13 CR1 2 PS CG2 2 0 13.019 ; >> qtot 0 >> 14 CR1 2 PS CG3 2 0 13.019 ; >> qtot 0 >> 15 CR1 2 PS CG4 2 0 13.019 ; >> qtot 0 >> 16 CR1 2 PS CG5 2 0 13.019 ; >> qtot 0 >> 17 CH2 3 PSN CH2 3 0 14.027 ; >> qtot 0 >> 18 CH1 3 PSN CH 3 0 13.019 ; >> qtot 0 >> 19 C 3 PSN CB 3 0 12.011 ; >> qtot 0 >> 20 CR1 3 PSN CG1 3 0 13.019 ; >> qtot 0 >> 21 CR1 3 PSN CG2 3 0 13.019 ; >> qtot 0 >> 22 CR1 3 PSN CG3 3 0 13.019 ; >> qtot 0 >> 23 CR1 3 PSN CG4 3 0 13.019 ; >> qtot 0 >> 24 CR1 3 PSN CG5 3 0 13.019 ; >> qtot 0 >> 25 CH3 3 PSN CH3 3 0 15.035 ; >> qtot 0 >> >> [ dihedrals ] >> ; ai aj ak al funct c0 c1 >> c2 c3 c4 c5 >> 1 2 3 4 1 gd_1 >> 1 2 3 8 1 gd_1 >> 9 2 3 4 1 gd_1 >> 9 2 3 8 1 gd_1 >> 1 2 9 10 1 gd_16 >> 3 2 9 10 1 gd_16 >> 2 3 4 5 1 >> 2 3 8 7 1 >> 2 9 10 11 1 gd_16 >> 9 10 11 12 1 gd_1 >> 9 10 11 16 1 gd_1 >> 17 10 11 12 1 gd_1 >> 17 10 11 16 1 gd_1 >> 9 10 17 18 1 gd_16 >> 11 10 17 18 1 gd_16 >> 10 11 12 13 1 >> 10 11 16 15 1 >> 10 17 18 19 1 gd_16 >> 10 17 18 25 1 gd_16 >> 17 18 19 20 1 gd_1 >> 17 18 19 24 1 gd_1 >> 25 18 19 20 1 gd_1 >> 25 18 19 24 1 gd_1 >> 18 19 20 21 1 >> 18 19 24 23 1 >> >> >> Cheers, >> 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 list gmx-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