I would suggest it, but I'm biased. (MMPBSA.py does get more support from
the list, though).
All the best,
Jason
On Tue, Aug 16, 2011 at 8:12 AM, <sribone.fcq.unc.edu.ar> wrote:
> I already have the ambertools1.5, are you suggesting the mmpbsa.py to
> calculate the binding energy??
> Thank you very much for your answer.
> Sergio.
>
> > 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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> >>
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> >>
> >
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> >
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 16 2011 - 06:30:03 PDT
