Okay, thanks very much for your answers, Prof. Case. Based on a
single quick test case, it looks like parmchk does like unique atom
names.
I will continue experimenting with antechamber and parmchk, as you've
suggested.
On Apr 16, 2009, at 8:29 AM, David A. Case wrote:
> On Wed, Apr 15, 2009, Nicholas Musolino wrote:
>
>> 1) Does parmchk require GAFF atomtypes? Or another atomtype format?
>
> Yes. It won't work with sybyl atom types, as you have discoverd.
>
>> 3) Do the atom names (field 2) need to be different for each atom,
>> e.g.
>> H1, H2, ... H10?
>
> This is needed for Amber, not sure about parmchk itself. Antechamber
> will create unique atom names if needed, but they may not make any
> chemical sense.
>
>>
>> More generally, I am able to produce MOL2 files of arbitrary
>> molecules
>> with (a) SYBYL atom type information and (b) bond information that I
>> deem trustworthy. What is the best way to obtain an FRCMOD file, and
>> then a PARM7 file, for later use with NAMD?
>
> The fact that you have sybyl atom types you like is not going to help
> much. Amber/antehcamber doesn't deal with the sybyl force field. As
> for the bonds, play with the "-j" flag for your problem molecules to
> see
> if that helps. If you have the ability, use energy minimization to
> get
> good geometries for molecules before sending them to antechamber.
>
> ...dac
>
>
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Received on Wed May 20 2009 - 11:22:53 PDT
