[gmx-users] Two [ dihedrals ] sections in topology

Lara Bunte lara.bunte at yahoo.de
Tue May 15 20:53:56 CEST 2012


>Is there some reason to believe you should not have dihedrals?  That doesn't 
>make much physical sense.

I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. 


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 17:02 Dienstag, 15.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology

On 5/15/12 10:43 AM, 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?

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
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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