VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 07 2011 - 19:25:54 CST

lara,

On Mon, Feb 7, 2011 at 7:23 PM, <larac_at_berkeley.edu> wrote:
> Hi,
>
> I am using VMD 1.8.7 and having trouble using the volmap command with ILS;
> I am able to get an output for volmap coulomb, but not volmap ILS.  I am
> unable to use the plug-in because I am using AMBER instead of CHARMM
> parameter
> files.  The command I use that fails is as follows:
>
> vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -dx output.dx
>
> The error reads:
> expected integer but got "atomselect9"volmap: molecule specified for
> ouput is invalid. (-mol)
>
> I am not sure where my syntax is wrong or if it is something about how I'm
> loading the AMBER parameters.  I am happy to provide more information if
> helpful.

looks like the syntax for volmap ils is different from the other
volmap variants:

vmd > volmap ils
wrong # args: should be "volmap ils <molid> <minmax> [options...]"

it is the calling sequence. you have to specify your parameters
as radius (sigma) and occupancy (epsilon), and of course you
have to convert them to CHARMM conventions. it would probably
be easiest to use the amber in charmm parameter file that has
been mentioned a few times on the list, IIRC.

>
> Any insight is very much appreciated!
> Lara Collazo
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.