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
Received on Wed Aug 19 2009 - 23:29:34 PDT
