Re: [AMBER] strip command usage in ptraj

From: <>
Date: Sun, 13 Mar 2011 23:30:26 +0800

hello, Adrian Roitberg,
I have tried the same ptraj input without strip command and i got the output binpos or mdcrd file contain 5000frames.

how do i know there are only 893 frames: I extract the pdb files from the binpos file every 25 frames, and the output says that only 893frames have been found!

and if i use binpos file as the output, it alway treats the whole output as one frame.

and to further deal with the problem, i just use VMD to look at the results and it goes to the same result!


发件人:Adrian Roitberg
发送日期:2011-03-13 23:23
收件人:AMBER Mailing List
主题: Re: [AMBER] strip command usage in ptraj

First, have you tried this same ptraj input WITHOUT the strip commands
and see how many frames you have ?

Second, how do you know there are only 893 frames instead of 5000 ?

On 3/13/11 4:14 PM, wrote:
> 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
> 2011-03-13
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida

on Sabbatical in Barcelona until August 2011.

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Received on Sun Mar 13 2011 - 09:00:04 PDT
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