AMBER Archive (2008)

Subject: AMBER: ptraj center problem

From: robaldo_at_dna.uba.ar
Date: Fri Nov 21 2008 - 11:31:27 CST

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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