From: larac_at_berkeley.edu
Date: Mon Feb 21 2011 - 13:59:40 CST

Thank you, Axel. I am still a bit confused about the syntax of -orient.
I have previously used -conf 50 to evaluate the probe at 50 different
rotational orientations. What is the equivalent expression with -orient?
I know n = 6 corresponds to 32 orientations but it is unclear to me from
the manual how to calculate n for 50 orientations.

Thank you for your patience.
Lara

> 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.
>