Can you send your script, the one you used again?
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: Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2009年10月14日,周三,下午3:32
Thank you for your suggestion. The result isn't changed as following and and I don't get the final results.
.......
.......
WARNING: Missing PB for PB in 0 -> Taken from -1
WARNING: Missing PB for PB in 1 -> Taken from 0
WARNING: Missing PB for PB in 2 -> Taken from 1
WARNING: Missing PB for PB in 3 -> Taken from 2
WARNING: Missing PB for PB in 4 -> Taken from 3
WARNING: Missing PB for PB in 5 -> Taken from 4
WARNING: Missing PB for PB in 6 -> Taken from 5
WARNING: Missing PB for PB in 7 -> Taken from 6
WARNING: Missing PB for PB in 8 -> Taken from 7
WARNING: Missing PB for PB in 9 -> Taken from 8
........
.......
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
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
No data for 0+2 PB PB 0
======= 2009-10-14 13:47:02 您在来信中写道：=======
>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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致
礼！
He Hongqing
leohhq.163.com
2009-10-14
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Received on Wed Oct 14 2009 - 01:30:02 PDT
