Dear All,
I am trying to study the interaction energy between residue 610 to the each of the residues (1-609) in the protein.
I heard I can use MM-GBSA to do the calculation, I tried but I am not sure if I have done it correctly.
I set the input file with following parameters:
DC=1
DCTYPE =2
COMREC=1-609
COMLIG=610-610
COMPRI=1-610
RECRES=1-609
RECPRI=1-609
LIGRES=1-1
LIGPRI=1.1
LIGMAP=610-610
After this I got files as listed at the end of this email.
I wonder if the DGtot in the COMPLEX section stands for the interaction energy between residue 610 and the each residue in the protein. If not, what does the value means, how can I found the interaction energy between residue 610 and each of hte residues in the protein?
I also noted that each title in the output files got two columns, e.g. there are two columns in SINT, what is the value in the second column under the same title means?
Best regards & thanks,
Cat,
Output file is listed below.
==>COMPLEX
Number
Residue
SINT
BINT
TINT
SVDW
BVDW
TVDW
SELE
BELE
TELE
SGAS
BGAS
TGAS
SGB
BGB
TGB
SGBSUR
BGBSUR
TGBSUR
SGBSOL
BGBSOL
TGBSOL
SGBTOT
BGBTOT
TGBTOT
0
.....
609
==>Receptor
0
....
608
==> LIGAND
0
==> DELTA
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Received on Mon Sep 14 2009 - 13:33:19 PDT
