Hello there,
I use Amber 10. The complex has protein residues from atom 1-5600, then
ligand 5601-5700, then water 5701-10000.
So in mm_pbsa input file, I have this:
NUMBER_LIG_GROUPS 1
LSTART 5601
LSTOP 5700
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 5600
RSTART 8000
RSTOP 8002
However, mm_pbsa failed as it complained "NATOM mismatch in coord and
topology file.
Ambpdb could not convert the extracted complex rst to pdb file either.
What is wrong? Do I need extra topology file for just the water
molecule?
Thanks,
Young
********************************************************
This communication and any files transmitted with it
may contain information that is confidential, privileged
and exempt from disclosure under applicable law. It is
intended solely for the use of the individual or entity
to which it is addressed. If you are not the intended
recipient, you are hereby notified that any use,
dissemination or copying of this communication is
strictly prohibited. If you have received this
communication in error, please notify the sender.
Thank you for your co-operation.
********************************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 08 2009 - 01:13:26 PDT
