Re: [AMBER] MMPBSA problem binding energy calculation

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Wed, 2 Jun 2010 09:35:25 +0900

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

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
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Received on Tue Jun 01 2010 - 18:00:03 PDT
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