From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 21 2011 - 15:17:52 CST

On Mon, Feb 21, 2011 at 2:59 PM, <larac_at_berkeley.edu> wrote:
> 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?

you have to ask the author of that code or read the source code.
i don't know. all i am telling you is what i can gather from quickly
glancing at the manual, knowing my way around the VMD sources,
and a bit of common sense.

> I know n = 6 corresponds to 32 orientations but it is unclear to me from
> the manual how to calculate n for 50 orientations.

i would use 50. as i said before, the -orient and the -conf flag are equivalent.
did you try using -orient 50 and did you see a difference.

perhaps you should try running some tests with a simpler system
where you know the results before trying something overly complicated.

axel.

> 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.
>>
>
>
>

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