VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 20 2011 - 12:32:15 CST

On Fri, Feb 18, 2011 at 1:10 PM, <larac_at_berkeley.edu> wrote:
> Thank you Axel; I will try that.  Any idea on the difference in usage of
> the -conf and -orient function?

you should use -orient. -conf is only provided for backward compatibility.

axel.

>
> 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.
>>
>
>
> 

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