VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 22 2011 - 08:37:16 CDT

On 03/22/2011 06:32 AM, Francesco Pietra wrote:
> Hi Peter:
>
> On Tue, Mar 22, 2011 at 1:42 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Hi Francesco,
>> Why are you surprised that a *gaff* topology doesn't match *charmm* atom
>> names and types?
> I showed that while asking to myself whether autopsf should be able to
> understand such gaff list or a charmm list is a must.

Hi Francesco,
psfgen (and thus autopsf) is completely agnostic regarding the force
field that you use, so long as you supply properly formatted topology files.

In your case, the atom names in your pdb do not match those in the
topology file. Thus, psfgen has no way of matching atoms in the pdb with
atoms in the topology, and makes extremely poor guesses instead. You
need to build your molecule in a way that gives proper atom names.

One way to guarantee proper naming is to build your molecule in
molefacture, and then use its typing functions to apply gaff
types/charges and write a topology file. It will handle the naming
automatically. This requires a little extra work to interface with
antechamber, as detailed on the molefacture web page. You can also just
do the renaming manually.

Best,
Peter