From: Prof. Eddie (eackad_at_siue.edu)
Date: Fri Jun 14 2013 - 11:35:33 CDT

I was using molfracture to start parameterizing a ligand using fftk. I
needed a psf file to first be generated. I need to use molfracture to
change the names since the pdb file was read in with plenty of mistakes
(Nitrogrens taken as Ni, Carbon alphas taken as Ca etc).

When molfracture generated the psf it decided on many of the types of atoms
(how they were bonded). To my eye, it seemed the psf it used had
4 characters for atom types (in column 6) compared with 5 characters when
using charmm36, such as CG31 instead of CG331.

How should I have done this? I simply want to create a psf file to start
the fftk process on a new ligand.
Eddie

On Tue, Jun 4, 2013 at 11:25 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> Probably in the peptide builder?
>
> Anyway, you could just run the pdb through psfgen but load in the new
> topology file and alias a couple of the atom names that changed.
>
> On Jun 4, 2013, at 10:12 AM, Mayne, Christopher G wrote:
>
> Where in Molefacture does the force field come into play? I don't know
> if all plugins use it, but the readcharmmpar plugin keeps a copy of
> CHARMM27 protein and CHARMM36 lipid parameters in the
> scripts/tcl/readcharmmpar1.2 folder.
>
> What, specifically are you trying to do?
>
> Regards,
>
> Christopher Mayne
>
>
> On Jun 4, 2013, at 7:12 AM, Prof. Eddie wrote:
>
> Anyone have any ideas? Is it hard coded?
>
>
> On Wed, May 29, 2013 at 3:32 PM, Prof. Eddie <eackad_at_siue.edu> wrote:
>
>> Hi all,
>> Is there a simple way to change the force-field that molfracture uses (or
>> even more broadly the parameter file for all vmd related things)? I'd like
>> to try using the charmm36 force field.
>> Thansk<
>> Eddie
>>
>> --
>> _________________________________________________________
>> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
>> Assistant Professor of Physics
>> Computational Nanophotonics
>> Southern Illinois University Edwardsville
>> (618) 650-2390
>>
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
>
>
>
>

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390