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
