[AMBER] Edit prmtop file

From: Paul Mortenson <P.Mortenson.astex-therapeutics.com>
Date: Wed, 13 Jul 2011 09:37:53 +0100

Dear AMBER users,

I have a prmtop file corresponding to an explicitly solvated protein,
and I would like to create a second prmtop file that is near identical,
but has exactly one fewer water molecules. I have been using the rdparm
program to do this, via the "stripwater" command, and it works fine when
the solvent is TIP3P, but not TIP4P - rdparm fails to recognise the
presence of any waters in this case. I have tested this for rdparm from
AMBER9, and also from AmberTools 1.5.

I have looked through the AmberTools manual, and cpptraj claims to be
able to write modified prmtop files, but with the caveat that they are
only suitable for visualisation, not simulation. I need to be able to
pass my modified prmtop file to sander.

Is there a way of doing this without having to write some code to modify
the prmtop file myself?


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Received on Wed Jul 13 2011 - 02:00:02 PDT
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