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Hi,
I'm trying to use ptraj and rdparm to strip some atoms out of a trajectory,=
and then output a prmtop file which corresponds to the edited coordinates.
I start 'rdparm prmtop.complex' and type
>ptraj ptraj_water.in
>writeparm prmtop.water
>quit
where 'ptraj_water.in' is a file containing the commands
>trajin mdcrd.1 1 50 10
>strip :1-25 =
=
>trajout water_rest restart
=
=
(which strips out all but my water molecules and ions, should=
you be interested).
The prmtop.water file I get has had no atoms stripped out of it, and is=
essentially the same as the starting prmtop.complex file, minus some=
comments. The 'strip' command has worked in one way though, because the=
water_rest.i files which are output are as expected.
Is it not actually possible for ptraj and rdparm to interact in this way,=
or have I missed a vital command somewhere? The alternative of using xleap=
to make the prmtop files separately should work, but leap keeps crashing=
on me (possibly because I'm using a truncated octahedral box?), and this=
method would be simpler anyway.
Thanks
Dave Evans
London School of Pharmacy
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Received on Tue Mar 16 2004 - 09:53:01 PST
