Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 15 Aug 2011 13:48:50 -0700

I suggest that you download the latest ambertool (1.5). It's free and
much better supported ...

All the best,
Ray

On Mon, Aug 15, 2011 at 8:04 AM, <sribone.fcq.unc.edu.ar> wrote:
> Dear all, Im writing because I've been trying to solve a problem with
> the mm_pbsa for months but I can not do it. When I calculate the
> binding energy for a ligand-enzime complex by mm_pbsa in amber10 using
> the following input:
>
> PREFIX                tr103-sr25
> PATH                  ./
> #
> COMPLEX               1
> RECEPTOR              1
> LIGAND                1
> #
> COMPT                 complejo.prmtop
> RECPT                 receptor.prmtop
> LIGPT                 ligando.prmtop
> #
> GC                    0
> AS                    0
> DC                    0
> #
> MM                    1
> GB                    1
> PB                    1
> MS                    1
> #
> NM                    0
> PROC                  2
> REFE                  0
> INDI                  1.0
> EXDI                  80.0
> SCALE                 1
> LINIT                 1000
> PRBRAD                1.4
> ISTRNG                0.0
> RADIOPT               0
> NPOPT                 1
> CAVITY_SURFTEN        0.0072
> CAVITY_OFFSET         0.00
> #
> SURFTEN               0.0072
> SURFOFF               0.00
>
> DIELC                 1.0
>
> IGB                   2
> GBSA                  1
> SALTCON               0.00
> EXTDIEL               80.0
> INTDIEL               1.0
> #
> SURFTEN               0.0072
> SURFOFF               0.00
>
> PROBE                 0.0
>
> I received the following problem:
>
> Use of uninitialized value in multiplication (*) at
> /home/sergio/Programas/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line
> 1378.
>     No data for 0+2 PB PB 0
>
> The output file gave me some warnings:
>  Reading tr103-sr25_com.all.out
>     WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>     WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>     WARNING: Missing EPB for PB in 0 -> Taken from -1
>     Reading tr103-sr25_rec.all.out
>     Checking CALC
>     WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>     WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>     WARNING: Missing EPB for PB in 0 -> Taken from -1
>     Reading tr103-sr25_lig.all.out
>     Checking CALC
>     WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>     WARNING: Missing PB for PB in 0 -> Taken from -1
>     WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>     WARNING: Missing EPB for PB in 0 -> Taken from -1
>
> The energy output for ligand, receptor and complex are:
> ligand
> MM
> GB
> PB
> MS
> 1
>  BOND    =        6.4620  ANGLE   =        9.0237  DIHED      =       15.3520
>  VDWAALS =       -4.9297  EEL     =        0.0000  EGB        =        0.0000
>  1-4 VDW =       16.1895  1-4 EEL =        0.0000  RESTRAINT  =        0.0000
> surface area =    594.734
> ECAVITY =    594.734
> EDISPER = 0.0000
>
> receptor
> MM
> GB
> PB
> MS
> 1
>  BOND    =     3076.6042  ANGLE   =     8300.7106  DIHED      =     9726.1992
>  VDWAALS =    -7614.1238  EEL     =   -73971.1573  EGB        =   -12444.1021
>  1-4 VDW =     3708.5404  1-4 EEL =    47222.5091  RESTRAINT  =        0.0000
> corrected reaction field energy:   -20517.454143
> surface area =  52994.258
> ECAVITY =  52994.258
> EDISPER = 0.0000
>
> complex
> MM
> GB
> PB
> MS
> 1
>  BOND    =     3083.0662  ANGLE   =     8309.7344  DIHED      =     9741.5536
>  VDWAALS =    -7655.2357  EEL     =   -73971.1573  EGB        =   -12436.3100
>  1-4 VDW =     3724.7299  1-4 EEL =    47222.5091  RESTRAINT  =        0.0000
> corrected reaction field energy:   -20505.425856
> surface area =  52811.495
> ECAVITY =  52811.495
> EDISPER = 0.0000
>
> I patched the bugfixes for amber. I've been running mm_pbsa for others
> very similar ligands, but I never had this problem before.
> I appreciate any kind of help or explanation about this problem.
> Thank you very much for your time.
>
> Sergio Ribone.
>
>
> Dept Pharmacy, Science Chemistry Phaculty
> National University of Córdoba
>
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Received on Mon Aug 15 2011 - 14:00:03 PDT
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