(unknown charset) [AMBER] strip command usage in ptraj

From: <asakiayumikio.gmail.com>
Date: Sun, 13 Mar 2011 23:14:46 +0800

Dear AMBER Mailing List,

I have simulated the prod. process for 20ns, before the analysis is carried out, i just want to transfer the mdcrd file to binpos.

and in trajin file i just want to use strip command to remove the wat and Cl-. however, i just want to keep one wat molecular for Hbond contaction analysis, so i write the input file as this:

trajin 1.mdcrd
trajin 2.mdcrd
trajin 3.mdcrd
trajin 4.mdcrd
trajin 5.mdcrd
trajin 6.mdcrd
trajin 7.mdcrd
trajin 8.mdcrd
trajin 9.mdcrd
trajin 10.mdcrd

strip :179-5156
strip :Cl-

trajout A.binpos binpos

the one molecular i want to keep is residue 178, but when i process this, it becomes wrong that the binpos file only contains 893 frames, while it should go to 5000.

Then i check the input file and change the output to mdcrd, and the problem still exists.

could you give the script how to deal with this problem?

thank you for your kind answer!

Best regards

AMBER mailing list
Received on Sun Mar 13 2011 - 08:30:04 PDT
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