Hi Dan,
After I upgrade ambertools to V1.5, all is correct now.
Thanks,
William
On 1/20/12, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I'm having a lot of trouble understanding your exact issue. It will
> help if you can post the exact ptraj input you are using that doesn't
> work for you. Also, what is the version number of the older ptraj you
> say works, and what is the version number of the new version you say
> doesnt work?
>
> -Dan
>
> On Fri, Jan 20, 2012 at 10:25 AM, Lianhu Wei <lianhu.wei.gmail.com> wrote:
>> Hi All,
>>
>> I have performed MD simulation for a protein in water for 60ns. With
>> older version I cam trajin all these file, then trajout the
>> trajectories in order, but with new version, the trajectories from
>> second mdcrd file will use the name as the first sets (prefix.number,
>> the number start from 1 again). So it replaced the trajectories from
>> the first mdcrd. So the trajectories I got is only the last set from
>> the last mdcrd file. Is there a solution for this?
>>
>> I tried to remove water and combined those trajectory to one file.
>> The I extract the trajectories from the combined file. But from about
>> 48ns, the structure got wield bond connection. I tried to extract
>> from the uncombined mdcrd files using the same procedure, the
>> trajectories are all okay. Does any had this problem? Is there any
>> clue for this?
>>
>> Thanks,
>> William
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
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Received on Fri Jan 20 2012 - 12:00:02 PST
