VMD-L Mailing List

From: larac_at_berkeley.edu
Date: Tue Feb 08 2011 - 15:15:48 CST

Hi Dr. Kohlmeyer,

I am afraid I'm still a bit confused--all of these variants fail and I
can't figure out the correct syntax from the manual.

vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -dx output.dx

vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -allframes
-combine pmf -dx output.dx -dihomo -probe1 -0.12 1.70 -bond 1.12 -conf 50
-cutoff 12 -subres 2

vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -allframes
-combine pmf -dx output.dx -dihomo -probe1 -0.12 1.70 -bond 1.12 -conf 50
-cutoff 12 -subres 2

The error is always:

expected integer but got "atomselect6"volmap: molecule specified for ouput
is invalid. (-mol)

Thanks for responding; I really appreciate it.
Lara

> 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.
>