AMBER Archive (2006)

Subject: AMBER: MMPBSA error

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Tue Jun 13 2006 - 09:52:08 CDT

Dear amber users

This is errors from mmpbsa. I generate three parameters files of LIG,REC and
COM. My mdcrd file is an explicit md including water. To do the mmpbsa, I
generate the snapshots from this parameters files for the first step but the
second step that all trajectories were calculated, I found errors which show
below. So, I don't understand where this errors happend.

Please help me for this problems.

Thanks

Jitrayut

[jitrayut_at_localhost 02_MMPBSA_Stability]$ /AMBER/amber9/exe/sander
-O -i sander_com.in -o sander_com.1.out -c
../01_GenerateSnapshots/enz_pep_pH7_com.crd.1 -p ../dock71.top not
successful
[2]- Exit 25 mm_pbsa.pl mm_pbsa.in >mm_pbsa.log

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 06/10/2006 at 18:27:42
  [-O]verwriting output

File Assignments:
| MDIN: sander_com.in
| MDOUT: sander_com.1.out
|INPCRD: ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1
| PARM: ../dock71.top
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 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 = 05/28/06 Time = 19:45:26
 NATOM = 27939 NTYPES = 16 NBONH = 26195 MBONA = 1781
 NTHETH = 3825 MTHETA = 2437 NPHIH = 7403 MPHIA = 4752
 NHPARM = 0 NPARM = 0 NNB = 51578 NRES = 8402
 NBONA = 1781 NTHETA = 2437 NPHIA = 4752 NUMBND = 46
 NUMANG = 92 NPTRA = 42 NATYP = 31 NPHB = 1
 IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

 Implicit solvent radii are modified Bondi radii (mbondi)

| Memory Use Allocated
| Real 1788610
| Hollerith 176038
| Integer 617374
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 17072 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

   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
     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
     Setting ifbox to 3 for non-orthogonal unit cell
| INFO: Old style inpcrd file read

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

  FATAL: NATOM mismatch in coord and topology files

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