AMBER Archive (2009)

Subject: [AMBER] ***PROBLEMS WITH GROUPLRES

From: Maria Mirza (maryamirza_at_gmail.com)
Date: Tue Aug 18 2009 - 19:34:41 CDT

Hello Amber Users

I am trying to run pairwise energy decomposition on a protein + drug system,
and I was consistently getting a "Missing BELE for MM 1" error for residue
269 (which is the last res in my receptor, residue 270 is the ligand). While
debugging it, I saw that the sander output files produced during the mm_pbsa
run do not have group assignments properly.

My mm_pbsa.in file for the decomposition run has the following
DCTYPE 4
#
COMREC 2-269
COMLIG 270-270
COMPRI 2-270
RECRES 2-269
RECPRI 2-269
RECMAP 2-269
LIGRES 1-1
LIGPRI 1-1
LIGMAP 270-270

However, in the sander output file for the complex, I see the following:

" LOADING THE DECOMP ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Residues considered as REC
      Number of atoms in this group = 0
    ----- READING GROUP 2; TITLE:
 Residues considered as LIG
      ***PROBLEMS WITH GROUPLRES 270 270 0 0 0 0 0 0
0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- READING GROUP 3; TITLE:
 Residues to print
 GRP 3 RES 2 TO 269"
.

I am not sure what is wrong with group specification and how to fix it. I am
attaching both the input file to mm_pbsa for decomposition, and the
subsequent input to sander (generated by mm_pbsa on the fly). as well.

Any help would be much appreciated.
regards
Maria





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