AMBER Archive (2009)

Subject: [Amber]AMBER: MM_PBSA problems in AMBER10

From: He Hongqing (leohhq_at_163.com)
Date: Tue Oct 13 2009 - 22:43:57 CDT

AMBERDear all,
 
 When I calculate the binding energy of protein-ligand complex by MM_PBSA in AMBER10. Input file is as following:
@GENERAL
PREFIX 123
PATH .././11
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./12.top
RECPT ./1.top
LIGPT ./2.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
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.00542
SURFOFF 0.92
@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
@MM
DIELC 1.0
@MS
PROBE 0.0
@PROGRAMS

output file is as following:

............
.............
    Processing PB PBSOL
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
    Processing PB PBELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
    No values for MM_GAS existing -> Skipping
    Processing MM GAS
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
    Processing GB GBTOT
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
=>> Calc delta from raw data

and

 Use of uninitialized value in multiplication (*) at /home/hehq/software/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /home/hehq/software/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /home/hehq/software/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /home/hehq/software/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
    No data for 0+2 PB PB 0

 Is there any body know why and how can I modify it?

Thanks

 
        
                                            

He Hongqing
leohhq_at_163.com
2009-10-14

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