Hi Paul,
Yes, you could use remove in tleap - you'd still need to read in a pdb (with
all waters) with loadpdb though. (Also carefully check if the residue number
of the water you want to delete is the same in tleap as it is from your
script)
Yes, just make sure you load all necessary parameters/topology.
For using TIP4P for you WAT molecules, see section 2.11 in the Amber Tools
manual.
Note that you can pass a script to tleap that does all you need, so you can
script the whole thing - i.e. take the water residue number you got from
your existing script and using that in your tleap script.
Good luck,
Marc
On 13 July 2011 10:14, Paul Mortenson <P.Mortenson.astex-therapeutics.com>wrote:
>
> 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 - 03:30:03 PDT
