perhaps this tutorial is from before ptraj did clustering. I suggest
using ptraj.
On Wed, Aug 10, 2011 at 5:32 AM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Sir/Madam,
> I am learning how to do cluster based on Prof. Rosswalker's tutorial. http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/section6.htm
> For my own study, I have converted my mdcrd files to one single binpos using ptraj. This binpos file should include all the atoms in the trajectory (0 to 100 ps), i.e. residues 1 to 60000.
> Then, i want to convert them into PDB file with the followings conditions.
> (1) As memory problems raised, I want to cut the number of PDB files to be analysis by 5 folds, i.e. only one out of the five snapshots were converted to a PDB file. Let's say a total of 100 snapshots were stored in the mdcrd file, I only want to choose 1, 5th, 10th, 15th.....snapshots to be converted to PDB format.
> How to do modify this commands to get this results?
> trajin xxx.mdcrd.gztrajout xxx.binpos binpos
> (2) Out of the 60000 residues, I am only interested to study clustering analysis based on the rmsd or contact analysis for the residue 200-1000 and 3000 to 3500. Should I do it in the step where I convert file to PDB or should I do it when I in the clustering step? Could you mind to give me a hand how to do so? As I found it difficult to I am now interested to analysis the two loops in a proteins that is not directly connected. In the following command line, how can I define I am only interested to study the rmsd for residue 200-1000 and 3000-3500?
> kclust -mode rmsd -centroid -cdist -heavy -lsqfit \
> -radius 6 -maxerr 1 -iterate \
> ../clustfils > ../Centroid_6
> Best regards,
> Catherine
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Received on Wed Aug 10 2011 - 04:30:02 PDT
