AMBER Archive (2009)

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

From: Ray Luo (ray.luo_at_uci.edu)
Date: Wed Oct 14 2009 - 11:48:48 CDT

Dear Hongqing,

First, have you patched the bugfixes for Amber10? If yes, let's see
whether you can reproduce your problem after cleaning up everything from
the working directory. Somehow a call to sander to get MM energy failed
once during the calculation ...

Also, it would be really helpful to show us your .out files, which
contain all the energy printouts from sander and pbsa.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

He Hongqing wrote:
> 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
>
> ------------------------------------------------------------------------
>
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