Re: [AMBER] strip command usage in ptraj

From: <asakiayumikio.gmail.com>
Date: Sun, 13 Mar 2011 23:47:13 +0800

Adrian Roitberg,!

Yes, i am certain that i use the same top file, which was used for MD calculation!


        2011-03-13
        
        asakiayumikio.gmail.com





发件人:Adrian Roitberg
发送日期:2011-03-13 23:41
收件人:AMBER Mailing List
抄送:
主题: Re: [AMBER] strip command usage in ptraj
ok, now.. did you load the SAME prmtop as before the ptraj when viewing in vmd or using ptraj to extract the pdbs ? On 3/13/11 4:30 PM, asakiayumikio@gmail.com wrote: > 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! > > > > 2011-03-13 > > asakiayumikio@gmail.com > > > > > > 发件人:Adrian Roitberg > 发送日期:2011-03-13 23:23 > 收件人:AMBER Mailing List > 抄送: > 主题: Re: [AMBER] strip command usage in ptraj > Hi > > 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, asakiayumikio@gmail.com 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 >> >> asakiayumikio@gmail.com >> 2011-03-13 >> _______________________________________________ >> AMBER mailing list >> AMBER@ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > -- Dr. Adrian E. Roitberg Associate Professor Quantum Theory Project, Department of Chemistry University of Florida on Sabbatical in Barcelona until August 2011. Email roitberg@ufl.edu _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Mar 13 2011 - 09:00:07 PDT
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