Thanks, Marc. In general the system may be a little more complicated
than just a protein - I may have included cofactors or other small
molecules parameterised by antechamber. I guess if I load the parameters
for these first it should work? An even quicker way would be if I could
generate both files from tleap in the first place - looks like the
remove command might do what I want. Unfortunately I'll have to get the
residue number programmatically (this is being called from a script) but
I think that should be possible.
One further question - how can I specify in tleap that the "WAT"
residues from the PDB file correspond to TIP4P (or any specific water
model)?
Thanks,
Paul
-----Original Message-----
From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
Sent: 13 July 2011 09:49
To: AMBER Mailing List
Subject: Re: [AMBER] Edit prmtop file
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)
Marc
On 13 Jul 2011 09:38, "Paul Mortenson"
<P.Mortenson.astex-therapeutics.com>
wrote:
> 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 - 02:30:03 PDT
