Re: [AMBER] MMPBSA problem binding energy calculation

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Jun 2010 20:43:14 -0400

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
Received on Tue Jun 01 2010 - 18:00:05 PDT
Custom Search