[gmx-users] Two [ dihedrals ] sections in topology
Justin A. Lemkul
jalemkul at vt.edu
Tue May 15 17:02:55 CEST 2012
On 5/15/12 10:43 AM, Lara Bunte wrote:
> 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?
Normally pdb2gmx will generate proper dihedrals based on bonded connectivity.
Is there some reason to believe you should not have dihedrals? That doesn't
make much physical sense.
> Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology?
What you've been defining as "empty" is not necessarily so. The fact that
parameters are not explicitly printed is not inherently indicative of a problem,
since the parameters are looked up from ffbonded.itp and not necessarily
recapitulated in the topology. If you get fatal errors about missing
parameters, that's a separate issue.
>>> [ 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?
Look in charmm27.ff/aminoacids.rtp.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users