[AMBER] Group specification for energy decomposition in thermodynamic integration

From: Joel Dockray <bsjpd.leeds.ac.uk>
Date: Mon, 7 Jan 2013 18:24:57 +0000

I'm still having difficulty with group specification for energy decomposition in thermodynamic integration.

This works:

my test group

RES 1 3

END

END

This does not:

my test group
FIND
* * * *
SEARCH

RES 1 3
END
END

Any ideas?



Here is the complete input for the failing process:

Constant temperature constant pressure
 &cntrl
  nstlim=90000, dt=0.002, ntx=5, irest=1, ntpr=100, ntwr=90000, ntwx=5000,
  temp0=300, ntt=3, gamma_ln=5, ig=48189117, taup=5.0,
  ntb=2, ntp=1, ntc=2, ntf=2, nrespa=1, idecomp=1,
  icfe=1, clambda=0.5, crgmask=':LIG.O5,O6,O7,H16,H17,H23,H24,H32', scmask='', ifsc=0
 &end
my test group
FIND
* * * *
SEARCH
RES 1 3
END
END

Here is the end of the output of the failing process. It looks like the FIND keyword is not being recognised. Why?

    LOADING THE DECOMP ATOMS AS GROUPS
    ----- READING GROUP 1; TITLE:
 my test group
      ***PROBLEMS WITH GROUPFIND 0 0 0 0 0 0 0 0 0 0 0 0 0 0*******

     rfree: Error decoding variable 2 2 from:
* *
     this indicates that your input contains
      incorrect information
     field 2 was supposed to
      have a (1=character, 2=integer, 3=decimal) value



Thank you!



Regards,

Joel Dockray
University of Leeds, UK


________________________________________
From: Joel Dockray [bsjpd.leeds.ac.uk]
Sent: 06 January 2013 00:51
To: amber.ambermd.org
Subject: [AMBER] rfree parsing error in group specification

Hello!

I'm using energy decomposition for the first time in a thermodynamic integration run.
I believe that there is an error in the FIND section of my first group specification.
The output is below. Any assistance you can give would be much appreciated.
Thank you!

Regards,
Joel Dockray
University of Leeds, UK


          -------------------------------------------------------
          Amber 10 SANDER 2008
          -------------------------------------------------------

| Run on 01/06/2013 at 00:17:18
  [-O]verwriting output

File Assignments:
| MDIN: MDInstructionsSim1.in
| MDOUT: /nobackup/bsjpd/TIProd/Temp19O1/Section1-0.out
|INPCRD: /nobackup/bsjpd/TIProd/Temp19O1/Restart1.rst
| PARM: /nobackup/bsjpd/TIProd/Temp19O1/Parameters1.prm
|RESTRT: /nobackup/bsjpd/TIProd/Temp19O1/Section1-0.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: /nobackup/bsjpd/TIProd/Temp19O1/Section1-0.crd
|MDINFO: /dev/null
|INPDIP: inpdip
|RSTDIP: rstdip

|INPTRA: inptraj
|

 Here is the input file:

Constant temperature constant pressure
 &cntrl
  nstlim=90000, dt=0.002, ntx=5, irest=1, ntpr=100, ntwr=90000, ntwx=5000,
  temp0=300, ntt=3, gamma_ln=5, ig=48189117, taup=5.0,
  ntb=2, ntp=1, ntc=2, ntf=2, nrespa=1, idecomp=1,
  icfe=1, clambda=0.5, crgmask='', scmask='', ifsc=0
 &end
Waters
FIND
* * * WAT
SEARCH
RES 1 9999
END
Ions
FIND
* * Na+ *
* * Cl- *
SEARCH
RES 1 9999
END
Ligand
FIND
* * * LIG
SEARCH
ATOM -1 999999
END
Residues
FIND
* * * GLY
* * * MET
* * * LEU
* * * GLU
* * * ALA
* * * THR
* * * ILE
* * * GLN
* * * LYS
* * * ASP
* * * TYR
* * * ARG
* * * PHE
* * * ASN
* * * VAL
* * * PRO
* * * SER
* * * HIE
* * * CYS
SEARCH
RES -1 9999
END
END


--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 16.718
| New format PARM file being parsed.
| Version = 1.000 Date = 01/05/13 Time = 18:44:36
 NATOM = 4805 NTYPES = 12 NBONH = 4755 MBONA = 52
 NTHETH = 82 MTHETA = 71 NPHIH = 156 MPHIA = 101
 NHPARM = 0 NPARM = 0 NNB = 6744 NRES = 1574
 NBONA = 52 NTHETA = 71 NPHIA = 101 NUMBND = 19
 NUMANG = 32 NPTRA = 21 NATYP = 14 NPHB = 1
 IFBOX = 1 NMXRS = 88 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 329722
| Hollerith 30406
| Integer 129674
| Max Pairs 533888
| nblistReal 57660
| nblist Int 194337
| Total 6496 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

O1Scaf-o11-o19-o37.0[1]

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 90000
     iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 1, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 90000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig =48189117
     temp0 = 300.00000, tempi = 0.00000, gamma_ln= 5.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 5.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Free energy options:
     icfe = 1, ifsc = 0
     klambda = 1
     clambda = 0.50000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 33.435 Box Y = 41.963 Box Z = 35.527
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 36 NFFT2 = 45 NFFT3 = 36
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

| MPI Timing options:
| profile_mpi = 0

    LOADING THE DECOMP ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Waters
      ***PROBLEMS WITH GROUPFIND 0 0 0 0 0 0 0 0 0 0 0 0 0 0*******


     rfree: Error decoding variable 2 2 from:
* *

     this indicates that your input contains

      incorrect information

     field 2 was supposed to

      have a (1=character, 2=integer, 3=decimal) value



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Received on Mon Jan 07 2013 - 10:30:03 PST
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