Hi
I am facing a problem in MM/PBSa calculation. Now, I am using perl scrip in
amber 11.0 and the problem is in snapshot generation. The snapshots have
very weird structure of the ligand. I have checked all the parm files
(complex, protein, ligand) and atom numbers in input scripts and everything
seems right. I had MD with 2 ligands and trying to compute the binding
energy one by one, when second some will be part of receptor.
. Marked section is like:
BOX YES
NTOTAL 37807 # total no of atoms (including water and
Ions) in traj file
#
NUMBER_LIG_GROUPS 1
LSTART 3923 # Beginning of Ligand one (26 atoms only)
LSTOP 3948 # end of ligand one
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 3922 # end of receptor
RSTART 3949 # beginning of ligand 2, which is a part of
receptor (26*5 atoms)
RSTOP 4078 # end of ligand 2
What could be the way to debut the problem ? why the ligands (both lig-1 and
lig-2 ) are are getting wrong connectivity in snapshots of complex. receptor
as well as ligand ? am I doing some blunder mistake ?
Sincerely
mish
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Received on Mon Mar 21 2011 - 10:30:02 PDT
