Re: [AMBER] MMPBSA problem binding energy calculation

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Wed, 2 Jun 2010 10:24:12 +0900

Hello Dr. Jason,

Thank you. I will check and run the calculations again with suitable prmtop
file.

Regards,
kamleshh

On Wed, Jun 2, 2010 at 9:43 AM, Jason Swails <jason.swails.gmail.com> wrote:

> Hello,
>
> On Tue, Jun 1, 2010 at 8:35 PM, kamlesh sahu <kamleshsemail.gmail.com
> >wrote:
>
> > Hello Dr. McGee,
> >
> > This is sander_com.1.out file ---->
> >
> >
> > -------------------------------------------------------
> > Amber 10 SANDER 2008
> > -------------------------------------------------------
> >
> > | Run on 06/01/2010 at 18:48:49
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: sander_com.in
> >
> > | MDOUT: sander_com.1.out
> >
> > |INPCRD: ./snapshot_com.crd.1
> >
> > | PARM: ./MEK_vac.prmtop
> >
> > |RESTRT: restrt
> >
> > | REFC: refc
> >
> > | MDVEL: mdvel
> >
> > | MDEN: mden
> >
> > | MDCRD: mdcrd
> >
> > |MDINFO: mdinfo
> >
> > |INPDIP: inpdip
> >
> > |RSTDIP: rstdip
> >
> >
> > |INPTRA: inptraj
> >
> > |
> >
> > Here is the input file:
> >
> > File generated by mm_pbsa.pl. Using MM GB
> >
> > &cntrl
> >
> > ntf = 1, ntb = 0, dielc = 1.0,
> >
> > idecomp= 0,
> >
> > igb = 2, saltcon= 0.00,
> >
> > offset = 0.09,
> >
> > intdiel= 1.0, extdiel= 80.0,
> >
> > gbsa = 0, surften= 1.0,
> >
> > cut = 999.0, nsnb = 99999,
> >
> > scnb = 2.0, scee = 1.2,
> >
> >
> >
> > imin = 1, maxcyc = 1, ncyc = 0,
> >
> > &end
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> >
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 05/31/10 Time = 13:15:47
> > NATOM = 7371 NTYPES = 19 NBONH = 3954 MBONA = 3480
> > NTHETH = 7823 MTHETA = 4688 NPHIH = 14694 MPHIA = 11713
> > NHPARM = 0 NPARM = 0 NNB = 38527 NRES = 602
> > NBONA = 3480 NTHETA = 4688 NPHIA = 11713 NUMBND = 66
> > NUMANG = 137 NPTRA = 56 NATYP = 50 NPHB = 1
> > IFBOX = 0 NMXRS = 49 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> > Implicit solvent radii are modified Bondi radii (mbondi)
> >
> >
> > | Memory Use Allocated
> > | Real 472444
> > | Hollerith 44830
> > | Integer 384211
> > | Max Pairs 1
> > | nblistReal 0
> > | nblist Int 0
> > | Total 5366 kbytes
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> >
> >
> >
> --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> >
> > General flags:
> > imin = 1, nmropt = 0
> >
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> > Nature and format of output:
> > ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
> > 500
> > iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> > 0
> > ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> > 0
> >
> > Potential function:
> > ntf = 1, ntb = 0, igb = 2, nsnb =
> > 99999
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> > saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000
> > gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000
> > rdt = 0.00000, rgbmax = 25.00000 extdiel = 80.00000
> > alpb = 0
> > scnb = 2.00000, scee = 1.20000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Energy minimization:
> > maxcyc = 1, ncyc = 0, ntmin = 1
> > dx0 = 0.01000, drms = 0.00010
> > | INFO: Old style inpcrd file read
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> > FATAL: NATOM mismatch in coord and topology files
> >
>
> Here is your problem. Your coordinate and topology files do not match.
> Make sure your prmtops are compatible with your coordinate files.
>
> Good luck!
> Jason
>
>
> >
> > Thank you
> > Best Regards,
> > kamlesh
> >
> > On Tue, Jun 1, 2010 at 10:55 PM, Dwight McGee <dwight.mcgee.gmail.com
> > >wrote:
> >
> > > What was in the sander_com1.out?
> > >
> > > T. Dwight McGee Jr.
> > >
> > >
> > > On Jun 1, 2010, at 5:42 AM, kamlesh sahu <kamleshsemail.gmail.com>
> > wrote:
> > >
> > > Dear amber users,
> > >>
> > >>
> > >> Hello
> > >> I need your help.
> > >>
> > >>
> > >>
> > >> I wish to calculate binding free energy for a complex. So I prepared
> > >> prmtop
> > >> files for the ligand and receptor (pdb contains 3 zinc ions). I also
> run
> > >> MD
> > >> simulation with the solvated complex structure containing ligand. When
> I
> > >> use
> > >> mm_pbsa.pl to calculate binding energy it gives following error-
> > >>
> > >>
> > >>
> > >> /home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
> > >> sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not
> > >> successful
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> The input files are ---
> > >> The extract_coords.mmpbsa file is as follows-
> > >>
> > >>
> > >> .GENERAL
> > >> PREFIX snapshot
> > >> PATH ./
> > >> COMPLEX 1
> > >> RECEPTOR 1
> > >> LIGAND 1
> > >> COMPT ./MEK_vac.prmtop
> > >> RECPT ./MEK_minus_SAM_vac.prmtop
> > >> LIGPT ./SAM_vac.prmtop
> > >> GC 1
> > >> AS 0
> > >> DC 0
> > >> MM 0
> > >> GB 0
> > >> PB 0
> > >> MS 0
> > >> NM 0
> > >> .MAKECRD
> > >> BOX YES
> > >> NTOTAL 3560
> > >> NSTART 1
> > >> NSTOP 200
> > >> NFREQ 1
> > >> NUMBER_LIG_GROUPS 1
> > >> LSTART 3359
> > >> LSTOP 3385
> > >> NUMBER_REC_GROUPS 1
> > >> RSTART 1
> > >> RSTOP 3355
> > >> .TRAJECTORY
> > >> TRAJECTORY ./md1.mdcrd
> > >> TRAJECTORY ./md2.mdcrd
> > >> .PROGRAMS
> > >>
> > >> I TRIED WITH SOME MODIFICATIONS OF THIS FILE ALSO.... LIKE IF I
> INCLUDE
> > Zn
> > >> IONS, RSTOP=3358,... but again the same error.
> > >>
> > >> The binding_energy.mmpbsa file -
> > >>
> > >> .GENERAL
> > >> PREFIX snapshot
> > >> PATH ./
> > >> COMPLEX 1
> > >> RECEPTOR 1
> > >> LIGAND 1
> > >> COMPT ./MEK_vac.prmtop
> > >> RECPT ./MEK_minus_SAM_vac.prmtop
> > >> LIGPT ./SAM_vac.prmtop
> > >> 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 0.0072
> > >> SURFOFF 0.00
> > >> .MM
> > >> DIELC 1.0
> > >> .GB
> > >> IGB 2
> > >> GBSA 1
> > >> SALTCON 0.00
> > >> EXTDIEL 80.0
> > >> INTDIEL 1.0
> > >> SURFTEN 0.0072
> > >> SURFOFF 0.00
> > >> .MS
> > >> PROBE 0.0
> > >> .PROGRAMS
> > >>
> > >> First I extracted the snapshots using command -
> > >>
> > >> $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
> > >>
> > >> Then I used following command to calculate binding energy -
> > >>
> > >> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> > >>
> > >> I got this error --->
> > >>
> > >> /home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
> > >> sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not
> > >> successful
> > >>
> > >>
> > >>
> > >> Kindly suggest me the ways to improve my calculation.
> > >>
> > >>
> > >>
> > >> Thank you
> > >>
> > >> Regards,
> > >>
> > >> kamlesh
> > >>
> > >>
> > >> --
> > >> Kamlesh Kumar Sahu
> > >> wako-shi (saitama)
> > >> _______________________________________________
> > >> 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
> > >
> >
> >
> >
> > --
> > Kamlesh Kumar Sahu (Ph.D. student)
> > Dept. of applied chemistry, Tohoku University graduate school of
> > engineering, Aoba-yama, Sendai
> > JAPAN
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Kamlesh Kumar Sahu (Ph.D. student)
Dept. of applied chemistry, Tohoku University graduate school of
engineering, Aoba-yama, Sendai
JAPAN
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Received on Tue Jun 01 2010 - 18:30:07 PDT
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