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 - 08:00:02 PST
