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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Received on Fri Dec 05 2008 - 16:16:19 PST
