"MM-PBSA script removes water molecules and ions automatically
(strip_mask)."
--I think that is just with the python script, from your other posts I think
the perl script is being used.
The perl script uses these:
NUMBER_LIG_GROUPS 1
LSTART 2622
LSTOP 3862
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 2621
If none of your counterions are defined in here they will be stripped with
the water.
Oliver
On 9 July 2010 12:29, Mahmoud A. A. Ibrahim <m.ibrahim.compchem.net> wrote:
> Dear Catein
> MM-PBSA script removes water molecules and ions automatically (strip_mask).
> Sincerely;
> M. Ibrahim
>
>
> On Fri, Jul 9, 2010 at 12:14 PM, Catein Catherine <askamber23.hotmail.com
> >wrote:
>
> >
> > Dear
> >
> >
> > Do I have to keep the Na+ counterions in prmtop and snapshot generation
> > when I do mmGBSA/PBSA calculation?
> >
> >
> >
> > I have done a calculation on a protein-drug system, for my MD
> calculation,
> > 20 salts and 20000 water molecules were added. However, when finish the
> > calculation. I want to calculate the mm-pbsa/gbsa energy. I understand
> I
> > need to exclude all the water molecule in extract snapshot and prepare
> free
> > of water prmtop files for energy.mmpbsa. How about the counterions that
> I
> > added? Should I also exclude all them in the snapshot and energy
> > procedures?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Cat
> >
> > _________________________________________________________________
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>
>
> --
> Mahmoud A. A. Ibrahim
> Current Address
> 7.05, School of Chemistry,
> The University of Manchester,
> Oxford Road, Manchester, M13 9PL,
> United Kingdom.
>
> Home Address
> Chemistry Department,
> Faculty of Science,
> Minia University,
> Minia 61519,
> Egypt.
>
> Contact Information
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Received on Fri Jul 09 2010 - 05:00:04 PDT
