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
