Hello,
I've put comments below:
On Thu, Aug 26, 2010 at 7:58 PM, William Flak <williamflak.yahoo.com> wrote:
> Dear AMBER
> During my data analysis, I had two problems with ptraj and couldn't
> overcome them.
> 1- Snapshot extracting: when I extracted a snapshot from my MD simulation,
> I got a structure half of my protein is out of the water box, I have done
> refit and image options.
> ****
> trajin Step1.mdcrd
> trajin Step2.mdcrd
> trajin Step3.mdcrd
> trajin Step4.mdcrd
> center :1-223
> mass origine
>
This should be mass origin, not mass origine, and it should be on the same
line as the "center" command.
center :1-223 mass origin
image origin center
> trajout Combined.mdcrd
> *****
> 2- Average structure:
> I had a 2ns simulation length partitioned on 4 mdcrd files. I combined
> these 4 mdcrd files and centered it using ptraj. I wanted to get the average
> strututre of the simulation. I got a structure with some groups
> cross-linked. These groups are free rotated groups e.g. CH3 group. is that
> right? or I made something wrong? How can I solve this problem in order to
> use the average structure for QM/MM optimization.
> Here is my ptraj command:
>
>
> trajin Step1.mdcrd
> trajin Step2.mdcrd
> trajin Step3.mdcrd
> trajin Step4.mdcrd
> center :1-223
> mass origine
> image origin center
> trajout Combined.mdcrd
>
> ***********
> trajin Combined.mdcrd
> strip :WAT
> average average_structure.pdb pdb
>
You should do an RMS before you average. Note that the manual says that
average does NOT implicitly RMS. However, you will see groups like CH3's
and carboxylate groups that have free rotation have atoms that effectively
"collapse" into one another since their average location is the same (you
can think of them as being rotationally degenerate in a local sense). It is
quite unlikely that the average structure will be appropriate for a QM/MM
optimization. I think your better option is to cluster and pull whatever
"representative" structure you deem most important. The literature may help
here as well, as may future commentators.
Good luck!
Jason
**********
>
> Any kind of help would be highly appreciated
> Thanks in advance
> W. Flak
>
>
>
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 26 2010 - 18:00:05 PDT
