Re: [AMBER] MMPBSA problem binding energy calculation

From: Bill Miller III <brmilleriii.gmail.com>
Date: Tue, 1 Jun 2010 21:35:03 -0400

Actually, I don't think the prmtop files are even used during the generating
coordinates step. So it doesn't matter what prmtop files you specify in when
GC=1, because the prmtop files won't be used. I'm pretty sure the only
things that are parameters used to create the coordinate files when GC=1 are
the numbers that you placed in the .MAKECRD section, which is why it is
important to make sure those number exactly match your prmtop files for the
next step (the binding energy calculation).

I hope that helps.

-Bill

On Tue, Jun 1, 2010 at 9:24 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:

> 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
> _______________________________________________
> 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
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Received on Tue Jun 01 2010 - 19:00:03 PDT
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