From: larac_at_berkeley.edu
Date: Fri Feb 18 2011 - 12:10:06 CST

Thank you Axel; I will try that. Any idea on the difference in usage of
the -conf and -orient function?

Many thanks,
Lara

> 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.
>