AMBER: Problem with energy decomposition in MMPBSA

From: <alfredoq.mail.fcq.unc.edu.ar>
Date: Tue, 05 Feb 2008 18:32:05 -0300

Dear Amber Community: I have been trying to perform an energy component
decomposition analysis on an trajectory obtained with sander, but I have
not been succesfull. I used the input script provided in the MMPBSA examples
folder (which runs ok in my machine), but when changing it to my needs, it
doesnt works. The trajectory corresponds to a complex with two residues, one is
the receptor and the other one is the ligand. In this way, I have prepared the
input file that I have attached, but when running it, it stopped with the error
"missing BELE for residue 1". Searching in the mailing list, I realized that
many people experienced this problem, but no answers to it were posted. So I
tried to find the error myself, and found that the problem occurs when sander
tries to make the corresponding computation over the ligand residue (I here
attach the output file). As can be seen, in the "READING GROUP 1; TITLE:"
section an unexpected error occurred, and in the "Residues to print" section,
"GRP 2 RES 2 TO 1" appeared although it should say GRP 2 RES 2
TO 2". Obviously, no atoms are selected, so no PRINT DECOMP - TOTAL
ENERGIES are printed, which finally originates the error. I have checked and
overchecked that in the corresponding input file I indicated LRES 2 2 and RES 2
2 (it is also printed in the header of the output file), but this error still
ocurrs.
Can anybody provide me some idea on what may be wrong?
Thanks in advance for the help
Best wishes,

Mario Alfredo Quevedo
Dpto. de Farmacia - Fac. de Ciencias Quimicas
Universidad Nacional de Cordoba
Argentina

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Facultad de Ciencias QuĂmicas - Universidad Nacional de CĂrdoba



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Received on Wed Feb 06 2008 - 06:07:36 PST
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