AMBER: rdparm/ptraj writeparm

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Date: Tue, 16 Mar 2004 08:57:16 +0000

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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

>writeparm prmtop.water

where '' 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.


Dave Evans
London School of Pharmacy
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Received on Tue Mar 16 2004 - 09:53:01 PST
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