AMBER Archive (2007)

Subject: AMBER: Error- MM_PBSA calculation

From: vikky 99 (vsaivikram_at_gmail.com)
Date: Wed Oct 10 2007 - 12:44:53 CDT

Dear Amber users,

I am using MM_PBSA module in amber9 for calculating the Free binding energy
of a complex (Protein + Inhibitor) using the following input file..

Input:

 @GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./actcdk2_complex.top
RECPT ./actcdk2_receptor.top
LIGPT ./h717_ligand.top
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
SURFTEN 0.00542
SURFOFF 0.92
@MM
DIELC 1.0
@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
@MS
PROBE 0.0
@PROGRAMS

While running the script i got the fallowing error message..

Script: mm_pbsa.pl binding_energy.mmpbsa >binding_energy.log

Use of uninitialized value in concatenation (.) or string at
/amber9/src/mm_pbsa/mm_pbsa_createinput.pm line 436.
Use of uninitialized value in concatenation (.) or string at
/amber9/src/mm_pbsa/mm_pbsa_createinput.pm line 436.
At line 270 of file _getcor.f (Unit 9 "./snapshot_com.crd.1")
Traceback: not available, compile with -ftrace=frame or -ftrace=full
Fortran runtime error: End of file
/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c
./snapshot_com.crd.1 -p ./actcdk2_complex.top not successful

 Kindly some one suggests me how to solve it.
Thanks in advance.
Sai vikrama chaitanya. V

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