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? Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? >> [ 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? 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
