AMBER Archive (2009)

Subject: [AMBER] Enquiry about MM/GBSA output file.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Sep 08 2009 - 02:14:19 CDT


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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