Re: [AMBER] Edit prmtop file

From: Marc van der Kamp <>
Date: Wed, 13 Jul 2011 09:48:59 +0100

How about simply writing a pdb with one less water (mod.pdb) and then use
leap, e.g. on tleap (after loading ff):

mol _ loadpdb mod.pdb
saveamberparm mol mod.parm mod.rst

( _ should be equals sign)

On 13 Jul 2011 09:38, "Paul Mortenson" <>
> 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?
> Thanks,
> Paul
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Received on Wed Jul 13 2011 - 02:00:04 PDT
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