AMBER Archive (2004)

Subject: AMBER: rdparm/ptraj writeparm

From: david.evans_at_ulsop.ac.uk
Date: Tue Mar 16 2004 - 02:57:16 CST

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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