VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Fri Jun 14 2013 - 12:05:46 CDT

Good to know! Thanks!
Eddie

On Fri, Jun 14, 2013 at 11:50 AM, Mayne, Christopher G <cmayne2_at_illinois.edu
> wrote:

> I'm not sure that Molefacture has a particularly sophisticated automated
> atom typing scheme (it might even use UFF). My suggestion is to use
> Molefacture to construct the ligand, manually set the atom names and types
> (via Molefacture's atom property edit features), and then write the
> PSF/PDB. If you use CGenFF-styled long atom types, you will need to
> manually modify the output PSF file header to include a "NAMD" tag. This
> will coerce VMD to read in the resulting PSF/PDB without truncating the
> atom types and garbling charges.
>
> Regards,
> Christopher Mayne
>
>
>
> On Jun 14, 2013, at 11:35 AM, Prof. Eddie wrote:
>
> 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
>
>
> 

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