AMBER Archive (2008)

Subject: AMBER: water in the binding site MMPBSA

From: jacopo.sgrignani_at_unifi.it
Date: Thu Apr 24 2008 - 08:51:43 CDT

Dear amber users,
I'm performing some MMPBSA computations but I have a little problem.
I have same protein ligand complexes where i need to conserve a water
molecule in the binding site during the mm-pbsa calculations.
I tried to use the script exctract_coordinates using this type of
instructions becouse between the first water molecule (the conserved
water) and protein there are the sodium ions:

NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 6888
RSTART 6889
RSTOP 6939

Moreover i prepared a topology with only the protein, the ligand and the
water molecule for the complex, but i can't start the computations. Now,
whitout a correct prmtop file, i can't check the crd files exctracted
to visualize the atoms that are really in the file.
Can anybody give me some advices.

Thanks a lot

Jacopo
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