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.163.com> 写道：
发件人: He Hongqing <leohhq.163.com>
主题: [Amber]AMBER: MM_PBSA problems in AMBER10
收件人: "AMBER" <AMBER.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.163.com
2009-10-14
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Received on Tue Oct 13 2009 - 23:00:02 PDT
