AMBER Archive (2007)

Subject: AMBER: Amber:PBSA&Extract_coords problem (Needed help)

From: odde (odde_at_olemiss.edu)
Date: Fri Apr 13 2007 - 14:06:42 CDT

Dear Sir,

I have simulated the system by considering crystal water
inside and which involves in hydrogen bonding with the
ligand and also with the receptor.

I am using the single trajectory protocol for the MM-PBSA.

I have converted my unsolvated complex (4FVC_62.prmtop) file
to pdb and looked inside as expected it also have counter
ions and crystal water…the question is when I extract
coordinates for my binding energy calculations

Should I take into account while numbering in
extract_coords.mmpbsa script?

In my Complex.prmtop (4FVC.prmtop) file the atom numbering
is as given
I have also attached pdb file of it for the clear picture)

1-8768 Receptor atoms

8769-8825 Ligand atoms

8826-8840 Counter ions (Chloride ions)

8841-9806 Crystal waters

Part of My extract_coords.mmpbsa script I made:
--------------------------------------------------

@MAKECRD
BOX YES
NTOTAL 76505
NSTART 1
NSTOP 300
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 8769
LSTOP 8825
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 8768
@TRAJECTORY

Is that right? But water molecules are not extracted when I
extract the coordinates,
Should I use two receptors instead one as in the above
script or is there any other way to extract these crystal
water molecules coordinates (8841-9806) for my binding
energy calculations.

Your kind response needed regarding the above.

Thanking you sir,

Dr. Srinivas Odde
University of Mississippi,
Department of Medicinal Chemistry,
417 Faser Hall, University, MS 38677,
U. S. A
Mobile: 662-801-0772: Lab: 662-915-1853
Email: odde_at_olemiss.edu


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