Hi,
There used to be some bugs in amber10, do you patch the latest bugfix.all files? You can have a try! Good luck!
Qinghua
________________________________
From: He Hongqing <leohhq.163.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wed, October 14, 2009 4:39:33 PM
Subject: Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10
I have got the result by the command, mm_pbsa_statistics.pl.
SAGE: mm_pbsa_statistics.pl <calc delta > <calc decomp >
<input file> <output file>
[<snap_min> <snap_max>]
Thanks again
======= 2009-10-14 16:18:34 您在来信中写道：=======
>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
>>
>>-----下面为附件内容-----
>>
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>
>>
>>
>>
>> ___________________________________________________________
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>
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>
>
>= = = = = = = = = = = = = = = = = = = =
>
>
> 致
>礼！
>
>
> He Hongqing
> leohhq.163.com
> 2009-10-14
>
>
>-----下面为附件内容-----
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd..org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
>http://card.mail.cn.yahoo.com/
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
= = = = = = = = = = = = = = = = = = = =
致
礼！
He Hongqing
leohhq.163.com
2009-10-14
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Received on Wed Oct 14 2009 - 02:30:07 PDT
