Dear Sir/Madam,
Thanks to the comments from Prof. Simmerling, I learnt to use the ptraj to do clustering, it works very well on clustering proteins based on rmsd.
Could you mind to give me some more guidance if I can also use ptraj to cluster proteins based on the residue contact maps? It seems to me that it could be done with MMTSB by the following command.
cluster.pl -maxnum 3 -mode contact -contmaxdist 8.0 xxx.pdb.*
Can I do something similar with ptraj? Many thanks in advance.
Catherine
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Received on Wed Aug 10 2011 - 10:00:03 PDT
