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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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