On Tue, 2012-05-15 at 15:43 +0100, Lara Bunte wrote: > Hi > > You wrote: > > >Two blocks of dihedrals are normal output for pdb2gmx - one for proper > >and one for improper dihedrals. > > > Is there a way to force pdb2gmx that there is only my block with improper > dihedrals in the topology? > Not that I'm aware of, and gromacs is designed to allow 2 dihedral blocks, I'd suggest you simply remove the block you do not want. Although you should be very sure that is what you want to do! > > Could that be a problem in further calculations, i.e. energy minimization if > there is this empty [ dihedrals ] block in the topology? > Not that I'm aware of; however, you should know that those missing parameters will be filled in with the dihedrals from the [ dihedral_types ] section above them in the .top file (this will most likely be in a #included file). > > >> [ bondedtypes ] > >> ; bonds angles dihedrals impropers > >> 1 1 5 5 > > > >Those are angle, dihedral and improper function types that are abnormal > >for CHARMM27. Using these in your .rtp means that you are no longer > >using CHARMM27. It might be reasonable for you to do this, but you need > >to be absolutely sure why. Importing a topology from another force field > >is not an acceptable reason. > > What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 > force field? > I don't know them but they will be in the CHARMM27.ff/amioacids.rtp file which should be in $GMXDATA/gromacs/top/
Richard > Thanks > > Greetings > > Lara > > > > > > > > ----- Ursprüngliche Message ----- > Von: Mark Abraham <mark.abra...@anu.edu.au> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > CC: > Gesendet: 12:57 Dienstag, 15.Mai 2012 > Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology > > On 15/05/2012 8:47 PM, Lara Bunte wrote: > > Hi > > > > After pdb2gmx I have two [ dihedrals ] sections in my topology. The first > > block is empty, the second block is correct with my parameters. > > > > > > An an example: > > > > > > First block: > > [ dihedrals ] > > ; ai aj ak al funct c0 c1 c2 > > c3 c4 c5 > > 2 1 19 8 5 > > 6 8 9 10 5 > > > > > > Second block: > > [ dihedrals ] > > ; ai aj ak al funct c0 c1 c2 > > c3 > > 1 8 6 4 5 180 100 > > 1 2 4 5 5 180 100 > > > > > > What could be the reason for this? What do I have to change in my force > > field folder (CHARMM27) to fix this? > > Two blocks of dihedrals are normal output for pdb2gmx - one for proper > and one for improper dihedrals. > > > > > In my .rtp file in the force field folder I have only this section for > > dihedrals > > > > [ impropers ] > > O4 N1 C2 N3 180 100 > > N1 C2 N3 H3 180 100 > > This produces your second block of type 5 dihedrals, given what you have > said below. > > > > > > > I declared my [ bondedtypes ] as the following: > > > > [ bondedtypes ] > > ; bonds angles dihedrals impropers > > 1 1 5 5 > > Those are angle, dihedral and improper function types that are abnormal > for CHARMM27. Using these in your .rtp means that you are no longer > using CHARMM27. It might be reasonable for you to do this, but you need > to be absolutely sure why. Importing a topology from another force field > is not an acceptable reason. > > Mark > -- > 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 > -- 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