VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Sun May 23 2010 - 15:52:11 CDT

Hi. Wich molecule is it? As i answeared here before, i've been using
paratools for my systems and has shown to be very efficient.

Depending on your system, you can generate bonds, angles, dihedrals and
impropers from topotool plugin 1.1 of VMD. I don't know the accuracy of the
impropers, but when i used it for bonds, angles and dihedrals it worked just
fine.

just download the latest plugin of topotools, version 1.1, and do something
like that:

package require topotools 1.1
topo retypebonds
topo guessangles
topo guessdihedrals
topo guessimpropers
set sel [atomselection top all]
$sel writepdb file.pdb
$sel writepsf file.psf

But the problem is, if you're gonna run it on NAMD, you'll need the
ForceFields parameters of angles, dihedrals and impropers, and it may be
hard to be found if you're dealing with an unusual system.

On Sun, May 23, 2010 at 5:53 AM, Hassan Shallal <hshallal_at_pacific.edu>wrote:

> Dear NAMD users,
>
> I am a new user of NAMD MD simulations. I know that NAMD doesn't have
> charmm parameter file for small molecules. I found a charmm parameter file
> for small molecules called *top_all36_cgenff.inp* (Reference: K.
> Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E.
> Darian, O. Guvench, P. Lopes, I. Vorobyov and A. D. Mackerell Jr., J.
> Comput. Chem., DOI: 10.1002/jcc.21367).
>
> The problem that I have is basically in generating psf file for the small
> molecule using the above parameters file, here are the two scenarios that I
> have tried and the description of why they didn't work:
>
> *Scenario 1:* I attempted to use VEGA software to generate an xplor PSF
> file of mHiy small molecule. It gerenated the file. However this file has a
> problem that makes VMD unable to merge it with the protein PSF file, what is
> that problem? As VMD says, the PSF file doesn't have cross terms.
> *My question is: is there any way that I can add cross terms to this psf
> file and make it acceptable by VMD? what are those cross terms? I looked in
> NAMD user manual and psfgen manual, couldn't find clear explanation of
> them...*
> **
> *Scenario 2:* I attempted to use VMD itself to generate the psf file of
> the small molecule by either issuing the corresponding commands in the TK
> console or using the Autopsf builder, everything seemed fine except for one
> little problem that blowed out the whole thing, VMD can't identify the *residue
> name*, the small molecule had a residue name of UNK, I changed that into
> MOL, it still didn't work..
> *Another question whose answer would otherwise solve the problem: how can
> I use a specific residue name for my small molecule that makes it recognized
> and then processed by VMD?*
> **
> I totally appreciate any feedback or advice
>
> Hassan Shallal
> University of the Pacific
> Stockton, CA 95211
>
>