From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 17 2011 - 13:54:49 CST

On Thu, Feb 17, 2011 at 1:13 PM, <larac_at_berkeley.edu> wrote:
> Hi,
> I am having 2 issues when running volmap ils.
>
> 1. What is the difference between the -conf and -orient function? Is one
> supposed to replace the other? If I would like the probe to be evaluated
> in 50 different rotational orientations, should I specify -conf 50 or
> -orient n with n = ??
>
> 2. I get the following error:
> ERROR) Found invalid VDW parameters 12: occupancy=-0.000000,
> radius=0.000000  when using the command:
> volmap ils 0 {{-68 -77 -80} {68 77 80}} -cutoff 12.0 -res 1 -subres 3
> -alignsel $sel -maxenergy 87 -T 300 -probecoor {{0.00 0.00 0.00} {0.00
> 1.23 0.00}} -probevdw {{-0.12 1.7} {-0.12 1.7}} dx output.dx
>
> My command specifies the VDW parameters of my probe and I have
> loaded/assigned an AMBER parameter file previously, so I am not sure what
> the problem is. Is there a way to get more information about what is
> missing?

please check whether you actually assigned all parameters correctly.
make you "amber" molecule the top molecule. then do
set amb [atomselect top all]
foreach {idx eps sig} [$amb get {index occupancy radius}] {
   puts "$idx $eps $sig"
}

that should give you a list of the assigned epsilon and sigma values
(keep in mind that VMD does 0-based indexing) and check if they
are correct. it looks as if for index 12, the epsilon is not set.

cheers,
   axel.

>
> Thank you very much,
> Lara
>
>

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