Date: Tue, 16 Mar 2004 10:04:47 -0700 (Mountain Standard Time)
From: "Thomas E. Cheatham, III"
Subject: Re: AMBER: rdparm/ptraj writeparm


> 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

The "writeparm" command is part of the rdparm functionality and knows
nothing of what happens in the ptraj part. In other words, the prmtop is
not affected by the strip command.

At present, your best option is to use tleap to read in a PDB and create a
new prmtop that corresponds to the stripped trajectory. I would run ptraj
again doing

trajin mdcrd.1 1 1 1
trajout snap.pdb pdb
strip :1-25

and then load in snap.pdb.1 into tleap.

There is a (undocumented) command in rdparm to strip some (but not ALL) of
the waters. The "testwater" command will create a new prmtop file with
any number of waters (> 0). The writeparm command is present to write
modified prmtop files that are modified by the commands to deletebonds,
deleteangles, deletedihedrals, ... Ideally in the future ptraj will have
prmtop writing capability, however this is still on the wish list.

--tom

p.s. if you are having trouble with xleap crashing, try tleap; it should
easily work to build the new prmtop based on reading of a PDB file. In
your case, if you are stripping the solute (i.e. :1-25) and building a
prmtop for just the solvent in a truncated octahedral geometry, you will
need to load the pdb and then build the box information; this is normally
done with the setbox command, however this will not work for truncated
octahedron. For this, you need to play with solvateOct setting a small
buffer and large closeness so that a box is built, but no water is added.
Good luck!