[AMBER] PairwiseDistance file location

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Thu, 4 Oct 2012 13:58:11 +0530

Dear Amber community member,
I'm using cluster command to perform clustering of the MD data.
To optimize cluster count I'm repeating the jobs with different desired
cluster counts and noting the DBI, pSF and SSR/SST values.

My question is how to give information about the PairwiseDistance file kept
in other folder for all the jobs? It is a big file and copying it every
time is not practical at my end.
Is there any flag in the cluster command to specify this file, I can't see
it in the AmberTools, Amber manual.

Can I run all the jobs from one ptraj input file, if so how? I tried this:

trajin xyz.mdcrd
cluster out cluster5 representative pdb average pdb averagelinkage clusters
5 rms .CA
cluster out cluster7 representative pdb average pdb averagelinkage clusters
7 rms .CA

But no PDB file is generated even after the first cluster command has
finished its jobs. So separate ptraj input files are necessary, are they?

Please suggest.
Thank you.

With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
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Received on Thu Oct 04 2012 - 01:30:06 PDT
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