AMBER Archive (2009)

Subject: Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Wed Oct 14 2009 - 04:22:41 CDT

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_at_163.com>
To: AMBER Mailing List <amber_at_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_at_163.com> 写道：
>
>发件人: He Hongqing <leohhq_at_163.com>
>主题: Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10
>收件人: "AMBER Mailing List" <amber_at_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_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
>>
>>-----下面为附件内容-----
>>
>>_______________________________________________
>>AMBER mailing list
>>AMBER_at_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_at_ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>= = = = = = = = = = = = = = = = = = = =
>           
>
>　　　　　　　　致
>礼！
>
>                 
>　　　　　　　　He Hongqing
>　　　　　　　　leohhq_at_163.com
>　　　　　　　　　　2009-10-14
>
>
>-----下面为附件内容-----
>
>_______________________________________________
>AMBER mailing list
>AMBER_at_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_at_ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber

= = = = = = = = = = = = = = = = = = = =
           

　　　　　　　　致
礼！

               
　　　　　　　　He Hongqing
　　　　　　　　leohhq_at_163.com
　　　　　　　　　　2009-10-14

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber