AMBER Archive (2008)

Subject: Re: AMBER: ptraj center problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 21 2008 - 12:42:17 CST

not sure why it isn't working- I use this and have no trouble

center :1-198 mass origin
image origin center familiar

do you have only one molecule in :1-24?
have you applied all patches?

On Fri, Nov 21, 2008 at 12:31 PM, <robaldo_at_dna.uba.ar> wrote:
> Dear amber users,
>
> I'm working in modified nucleic acid molecular dynamics. I use tleap to
> add ions and make an octahedral box water. Then, when I finish the dynamic
> and I try to make a center and complete trajectory file using the
> individual trajectories, ptraj doesn't center the water and the octahedral
> box lost shape. While I always use the same protocol and the same ptraj.in
> to do that, it only happens sometimes. Therefore, when I try to calculate
> the hydratation I have lots of errors.
>
>
> I'm using the following ptraj.in:
>
> #******* ptraj center
>
> rm -f ptraj.in
>
> cat <<eof > ptraj.in
>
> trajin ../x_3ns.tra
> trajin ../x_4ns.tra
> trajin ../x_5ns.tra
> trajin ../x_6ns.tra
> trajin ../x_7ns.tra
> trajin ../x_8ns.tra
> trajin ../x_9ns.tra
> trajin ../x_10ns.tra
>
> center :1-24
> image center byres familiar
> trajout x.tra
>
> eof
>
> ptraj ./x.top < ptraj.in > ptraj.out
>
>
> thanks,
>
> best regards,
>
> Laura
>
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