This input file just generates the snapshots that are used for the energy
calculations. Since MM, GB, PB, etc are all set to 0, not energy
calculations were performed. After running mm_pbsa.pl with this input file,
you should have 600 total snapshots (200 for com, 200 for rec, and 200 for
lig). Once these snapshots have been created, you should run
mm_pbsa.plagain using the binding_energy.mmpbsa input file that can be
found on the
tutorial's website (
http://ambermd.org/tutorials/advanced/tutorial3/section3.htm). Adapt
binding_energy.mmpbsa for your system before running the script. This should
do the actual energy calculations and create the statistics file you are
looking for.
-Bill
On Fri, Oct 29, 2010 at 10:10 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Thank you for your reply.
> I followed the tutorial and used the mmpbsa.pl script. But it didn't work
> out.
> I also tried mmpbsa_statistics.pl, but it didn't work neither. Maybe the
> problem is from some setting in my script.
>
>
>
> .GENERAL
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./com_vac.prmtop
> RECPT ./antibody_vac.prmtop
> LIGPT ./ricin.prmtop
> #
> GC 1
> AS 0
> DC 0
> #
> MM 0
> GB 0
> PB 0
> MS 0
> #
> NM 0
> #
> .MAKECRD
> #
> BOX YES
> NTOTAL 197191
> NSTART 150
> NSTOP 350
> NFREQ 1
> #
> NUMBER_LIG_GROUPS 1
> LSTART 1
> LSTOP 8217
> NUMBER_REC_GROUPS 1
> RSTART 8218
> RSTOP 21694
> #
> .TRAJECTORY
> #
> TRAJECTORY ./prod1.mdcrd
> TRAJECTORY ./prod2.mdcrd
> #
> .PROGRAMS
>
>
> Do you think this script has any problem?
> Thank you.
>
>
>
>
>
>
>
>
>
> ________________________________
> From: Dwight McGee <dwight.mcgee.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wed, October 27, 2010 7:11:27 PM
> Subject: Re: [AMBER] cannot generate snapshot_statistics.in file
>
> Hi,
>
> To gain more insight on how MMPBSA works you can start by reading the
> papers below. They offer great insight into the methodology and how the
> program works. If the manual is to brief, I would suggest going through the
> Amber tutorial on MMPBSA if you have not already done so.
> http://ambermd.org/tutorials/advanced/tutorial3/ . The tutorial walks you
> through step by step as to what setting GB, PB, or NM to 1 does. Hope that
> helps and good luck.
>
> 1. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D.
> A. J. Am. Chem. Soc. 1998, 120, 9401-9409.
> 2. Massova, I.; Kollman, P. A. J. Am. Chem. Soc. 1999, 121, 8133-8143
>
>
>
> On Wed, Oct 27, 2010 at 6:58 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > Hello,
> > When I run the binding_energy.mmpbsa, it showed error and stopped:
> > /usr/local/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out
> > -c
> > ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
> > This is the output in the log file:
> > =>> Init data
> > Presuming executables of amber suite to be in /usr/local/amber10/exe
> >
> > =>> Reading input parameters
> > Found PREFIX => snapshot
> > Found PATH => ./
> > Found COMPLEX => 1
> > Found RECEPTOR => 1
> > Found LIGAND => 1
> > Found COMPT => ./com_vac.prmtop
> > Found RECPT => ./ricin.prmtop
> > Found LIGPT => ./antibody_vac.prmtop
> > Found GC => 0
> > Found AS => 0
> > Found DC => 0
> > Found MM => 1
> > Found GB => 1
> > Found PB => 1
> > Found MS => 1
> > Found NM => 0
> > Found PROC => 2
> > Found REFE => 0
> > Found INDI => 1.0
> > Found EXDI => 80.0
> > Found SCALE => 2
> > Found LINIT => 1000
> > Found PRBRAD => 1.4
> > Found ISTRNG => 0.0
> > Found RADIOPT => 0
> > Found NPOPT => 1
> > Found CAVITY_SURFTEN => 0.0072
> > Found CAVITY_OFFSET => 0.00
> > Found SURFTEN => 0.0072
> > Found SURFOFF => 0.00
> > Found DIELC => 1.0
> > Found IGB => 2
> > Found GBSA => 1
> > Found SALTCON => 0.00
> > Found EXTDIEL => 80.0
> > Found INTDIEL => 1.0
> > Found SURFTEN => 0.0072
> > Found SURFOFF => 0.00
> > Found PROBE => 0.0
> >
> > =>> Checking sanity
> > Checking GENERAL
> > Setting START to default 1
> > Setting STOP to default 10e10
> > Setting OFFSET to default 1
> > Setting VERBOSE to default 0
> > Checking MM
> > Checking PB
> > Checking GB
> > Checking MS
> >
> > =>> Creating input
> > Sander input
> > PBSA input
> >
> > =>> Calculating energy / entropy contributions
> > Calc contrib for ./snapshot_com.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> >
> > I set MM, GB, PB, and NM to 1. It that right?
> > BTW, I don't know how these terms related to the binding energy
> > calculation. The
> > manual is too brief. I can't find much helpful information.
> >
> >
> >
> >
> >
> >
> >
> > ________________________________
> > From: Bill Miller III <brmilleriii.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Wed, October 27, 2010 11:57:58 AM
> > Subject: Re: [AMBER] cannot generate snapshot_statistics.in file
> >
> > The extract_coords.mmpbsa input file is designed to simply make the
> > snapshots that binding_energy.mmpbsa uses to actually calculate the
> > energies. You will need to turn on (set equal to 1) MM, GB, PB, etc in
> > order
> > to get the files you described below.
> >
> > -Bill
> >
> > On Wed, Oct 27, 2010 at 11:52 AM, bin wang <wang_p_z.yahoo.com.cn>
> wrote:
> >
> > > Dear all,
> > > When I run extract_coords.mmpbsa for a protein-antibody complex, the
> log
> > > file
> > > didn't show any error message, but I didn't get snapshot_com.all.out,
> > > snapshot_lig.all.out, snapshot_rec.all.out, and
> > snapshot_statistics.infile.
> > > Could anybody give me some suggestions?
> > >
> > > I got 200 snapshot file for the complex, ligand, and receptor, but no
> > > all.out
> > > files. The script worked for other molecules, I don't know why it
> didn't
> > > work
> > > this time.
> > >
> > > Thank you very much.
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 29 2010 - 08:00:04 PDT
