VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Jun 14 2013 - 11:50:10 CDT

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<mailto: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<mailto: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<tel:%28618%29%20650-2390>
--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390<tel:%28618%29%20650-2390>
--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390