AMBER Archive (2009)

Subject: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Wed Oct 14 2009 - 00:47:02 CDT

Hi,

I guess this should be your second time to run MM- PBSA in the same file, isn't it? If it is true, you can delete the file produced in the first time. And re-run frame extract step and energy calculation step, it will be ok.

Rilei Yu

--- 09年10月14日，周三, He Hongqing <leohhq_at_163.com> 写道：

发件人: He Hongqing <leohhq_at_163.com>
主题: [Amber]AMBER: MM_PBSA problems in AMBER10
收件人: "AMBER" <AMBER_at_ambermd.org>
日期: 2009年10月14日,周三,上午11:43

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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