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
Received on Sun Mar 13 2011 - 09:00:05 PDT
