Re: [AMBER] strip command usage in ptraj

From: <asakiayumikio.gmail.com>
Date: Sun, 13 Mar 2011 09:05:00 -0700 (PDT)

Adrian Roitberg!

I will try later and i will let you know as soon as possible

        2011-03-14
        
        asakiayumikio.gmail.com





发件人:Adrian Roitberg
发送日期:2011-03-13 23:57
收件人:AMBER Mailing List
抄送:
主题: Re: [AMBER] strip command usage in ptraj
well, then, that is your answer you are using a prmtop file with N atoms to extract the new trajectory. This new trajectory, by definition, has less atoms than the original, since you stripped a lot of them. So, you are trying to use the original prmtop with the new trajectory, which messes things up. You need a new prmtop file without the waters you stripped and without the chlorine atoms. Otherwise, you can use ptraj to save a pdb file for ONE frame. Then if you load that pdb file into vmd and then the binpos, everything you be ok let me know if this works On 3/13/11 4:47 PM, asakiayumikio@gmail.com wrote: > 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 t > o 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 > _______________________________________________ > 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 - 09:30:02 PDT
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