AMBER Archive (2009)

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

From: He Hongqing (leohhq_at_163.com)
Date: Wed Oct 14 2009 - 02:32:25 CDT

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-----
>
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　　　　　　　　致
礼！
 
                                 
　　　　　　　　He Hongqing
　　　　　　　　leohhq_at_163.com
　　　　　　　　　　2009-10-14


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