AMBER Archive (2009)

Subject: [AMBER] MM_PBSA decomp problem

From: B. Nandy (nandy_at_physics.iisc.ernet.in)
Date: Tue Sep 22 2009 - 07:29:23 CDT

Dear Amber user,

I am facing problem to get binding energy residue wise using decomp option.
My system contains one DNA and a dendrimer. And the problem is arising due
to this dendrimer molecule. The input file is following

@GENERAL
PREFIX snapshot
PATH
/home/bnandy/dna_dendrimer/workspace/65_s1_g4/mm_pbsa/decomp/
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT dna_den.top
RECPT dna.top
LIGPT gen4_pp.top
GC 0
AS 0
DC 1
MM 1
GB 1
PB 0
MS 0
NM 0
@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 200
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
@MM
DIELC 1.0
@GB
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
@DECOMP
DCTYPE 2
COMREC 1-76
COMLIG 77-77
COMPRI 1-77
RECRES 1-76
RECPRI 1-76
RECMAP 1-76
LIGRES 1-1
LIGPRI 1-1
LIGMAP 77-77
@MS
PROBE 0.0
SANDER $AMBERHOME/exe/sander
@PROGRAMS

And the error message is
"Missing TGB for GB in 1 (residue 77)"

In my case ligand is the dendrimer and the receptor is the DNA. All the
input files and the residue numbering seems to be ok. Searching the
archive I couldn't find the solution. Can someone please help me.

Many thanks
Bidisha 

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