AMBER Archive (2004)

Subject: AMBER: problems with extra points

From: German Sciaini (gsciaini_at_q1.fcen.uba.ar)
Date: Wed Jun 16 2004 - 11:29:45 CDT

>
> My name is German, I am using Amber7 to try to simulate a 216
> ammonia box.
>The model for ammonia molecule is very similar to tip4p for water, also
>rigid, but having one more site.
>I´ve already build all the files required by Sander using tleap...
>These are my files which are being used by tleap:
>
>file: amo.amb, initial coordinates
>
>ATOM 1 NG AMO 1 0.000 0.000 0.000
>ATOM 2 QG AMO 1 0.059 0.079 0.121
>ATOM 3 HG1 AMO 1 1.012 0.000 0.000
>ATOM 4 HG2 AMO 1 -0.291 0.970 0.000
>ATOM 5 HG3 AMO 1 -0.291 -0.390 0.888
>TER
>ATOM 6 NG AMO 2 0.000 0.000 4.141
>ATOM 7 QG AMO 2 0.059 0.079 4.262
>ATOM 8 HG1 AMO 2 1.012 0.000 4.141
>ATOM 9 HG2 AMO 2 -0.291 0.970 4.141
>ATOM 10 HG3 AMO 2 -0.291 -0.390 5.028
>TER
>ATOM 11 NG AMO 3 0.000 0.000 8.281
>ATOM 12 QG AMO 3 0.059 0.079 8.402
>ATOM 13 HG1 AMO 3 1.012 0.000 8.281
>ATOM 14 HG2 AMO 3 -0.291 0.970 8.281
>ATOM 15 HG3 AMO 3 -0.291 -0.390 9.169
>TER
> .......etc...
>
>file: frcmod.nh3, force field parameters for new atom types.
>This is the parameter set for nh3
>MASS
>NG 14.00
>EP 3.00
>HG 1.00
>
>BOND
>NG-EP 553.000 0.1560
>NG-HG 500.000 1.0124
>HG-HG 500.000 1.6243
>
>ANGLE
>HG-NG-HG 500.0 106.68
>HG-NG-EP 500.0 67.87
>
>NONBON
> NG 3.400 0.278
> HG 0.000 0.000
> EP 0.000 0.000
>
>file: prep.nh3, prep amber file
>
> 0 0 2
>
>Ammonia prep file
>Ammonia res
>AMO INT 0
>CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 0 0 0.0000 0.0000 0.0000
> 0.0
> 2 DUMM DU M 1 0 0 1.0000 0.0000 0.0000
> 0.0
> 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000
> 0.0
> 4 NG NG M 3 2 1 1.0000 90.0000
> 0.0000 0.0
> 5 QG EP E 4 6 3 0.1560 67.8700
> 0.0000 -1.386
> 6 HG1 HG E 4 3 2 1.0124 90.0000
> 0.0000 0.462
> 7 HG2 HG E 4 5 3 1.0124 106.6800
> 0.0000 0.462
> 8 HG3 HG E 4 5 3 1.0124 106.6800
> 180.0000 0.462
>
>DONE
>STOP
>
>source for tleap run:
>addAtomTypes {
> { "HG" "H" "sp3" }
> { "NG" "N" "sp3" }
> { "EP" "Lp" "sp3" }
> }
> loadamberprep prep.nh3
> amoniaco = loadamberparams frcmod.nh3
> saveoff amoniaco
> a = loadpdb amo.amb
> setbox a vdw
> saveamberparm a x.top x.crd
> savepdb a x.pdb
> quit
>
>file for Sander run:
>rm -f mdin
>cat <<eof > mdin
># sander: Eqlbrtn of NH3 const T , SHAKE, cut=14
> &cntrl
> IMIN=0, NTX=1, IREST=0, NTRX=1, NTXO=1,IBELLY=0, NTR=0,
> NTPR=1000, NTWR=100, IWRAP=1, NTWX=100, NTWV=100,
> NTWE=100000, IOUTFM=0, NTF=2, NTB=1, NTP=0, CUT=14,
> NSTLIM=1000, NSCM=100, T=0.0, DT=0.0001, TEMP0=450.0,
> TEMPI=450.0, NTT=1, TAUTP=1.0, VLIMIT=100,
> NTC=2, TOL=0.0000001, JFASTW=4,
> &end
> &ewald
> VERBOSE=1,
> EW_TYPE=0,
> NBFLAG=1,
> SKINNB=2.0,
> EEDMETH=1,
> FRAMEON=1,
> &end
>
>eof
>
>cp x.crd x.ref
>
>echo 'calen 1 running'
>
>sander -O -i mdin -o mdout -p x.top -c x.crd -r x.rst -ref x.ref -x x.tra
>-v x.vel -e x.ene
>mv mdout opt.mdout
>mv x.ene opt.ene
>mv x.tra opt.tra
>cp x.rst opt.crd
>mv x.rst x.crd
>echo 'calen 1 fin'
>
>#************************************************************
>
>The content of the sander output file is:
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
>| Wed Jun 16 10:12:32 2004
>
> [-O]verwriting output
>
>File Assignments:
>| MDIN:
>mdin
>| MDOUT:
>mdout
>|INPCRD:
>x.crd
>| PARM:
>x.top
>|RESTRT:
>x.rst
>| REFC:
>x.ref
>| MDVEL:
>x.vel
>| MDEN:
>x.ene
>| MDCRD:
>x.tra
>|MDINFO:
>mdinfo
>|INPDIP:
>inpdip
>|RSTDIP:
>rstdip
>
>
> Here is the input file:
>
># sander: Eqlbrtn of NH3 const T , SHAKE,
>cut=10.0
> &cntrl
>
> IMIN=0, NTX=1, IREST=0, NTRX=1, NTXO=1,IBELLY=0,
> NTR=0,
> NTPR=1000, NTWR=100, IWRAP=1, NTWX=100,
> NTWV=100,
> NTWE=1000, IOUTFM=0, NTF=3, NTB=1, NTP=0,
> CUT=1,
> NSTLIM=1000, NSCM=100, T=0.0, DT=0.0001,
> TEMP0=450.0,
> TEMPI=450.0, NTT=1, TAUTP=1.0,
> VLIMIT=100,
> NTC=3, TOL=0.0000001,
> JFASTW=4,
> &end
>
> &ewald
>
> VERBOSE=1,
>
> EW_TYPE=0,
>
> EW_COEFF=0.35,
>
> NBFLAG=1,
>
> SKINNB=2.0,
>
> EEDMETH=1,
>
> FRAMEON=1,
>
> &end
>
>
>
>
>--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>--------------------------------------------------------------------------------
>
>|
>Flags:
> getting new box info from bottom of inpcrd
>| peek_ewald_inpcrd: Box info found
>| New format PARM file being parsed.
>| Version = 1.000 Date = 06/16/04 Time = 10:11:05
> NATOM = 15 NTYPES = 2 NBONH = 9 MBONA = 3
> NTHETH = 9 MTHETA = 0 NPHIH = 0 MPHIA = 0
> NHPARM = 0 NPARM = 0 NNB = 33 NRES = 3
> NBONA = 3 NTHETA = 0 NPHIA = 0 NUMBND = 2
> NUMANG = 1 NPTRA = 0 NATYP = 3 NPHB = 0
> IFBOX = 1 NMXRS = 5 IFCAP = 0 NEXTRA = 3
>
>
>| EWALD MEMORY USE:
>
>| Total heap storage needed = 252
>| Adjacent nonbond minimum mask = 66
>| Max number of pointers = 25
>| List build maxmask = 132
> Number of grids per unit cell in each dimension:
> 6 6 15
> Unit cell edge lengths in each dimension:
> 6.800 6.800 15.081
> Distance between parallel faces of unit cell:
> 6.800 6.800 15.081
> Distance between faces of short range grid subcells:
> 1.133 1.133 1.005
> Resulting cutoff from subcell neighborhoods is 3.016
>| Maximage = 21
>
>| EWALD LOCMEM POINTER OFFSETS
>| Real memory needed by PME = 252
>| Size of EEDTABLE = 2624
>| Real memory needed by EEDTABLE = 10496
>| Integer memory needed by ADJ = 132
>| Integer memory used by local nonb= 42151
>| Real memory used by local nonb = 243
>
>| MAX NONBOND PAIRS = 10000000
>
>| Memory Use Allocated Used
>| Real 10000000 11817
>| Hollerith 1000000 95
>| Integer 10000000 52591
>
>| Max Nonbonded Pairs:10000000
>| Duplicated 0 dihedrals
>| Duplicated 0 dihedrals
>
> BOX TYPE: RECTILINEAR
>
>--------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>--------------------------------------------------------------------------------
>
>
>
>
>General flags:
> imin = 0, nmropt = 0
>
>Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
>Nature and format of output:
> ntxo = 1, ntpr = 1000, ntrx = 1,
> ntwr = 100
> iwrap = 1, ntwx = 100, ntwv = 100,
> ntwe = 1000
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
>Potential function:
> ntf = 3, ntb = 1, igb = 0,
> nsnb = 25
> ipol = 0, gbsa = 0
> dielc = 1.00000, cut = 1.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
>Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
>Molecular dynamics:
> nstlim = 1000, nscm = 100, nrespa = 1
> t = 0.00000, dt = 0.00010, vlimit = 100.00000
>
>Temperature regulation:
> ig = 71277, ntt = 1, vrand = 0
> temp0 = 450.00000, tempi = 450.00000, heat = 0.00000
> dtemp = 5.00000, tautp = 1.00000
>
>SHAKE:
> ntc = 3, jfastw = 4
> tol = 0.00000
>
>Extra-points options:
> frameon = 1, chngmask= 1
>
>Ewald parameters:
> verbose = 1, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, frc_int = 0,
> netfrc = 1
> Box X = 6.800 Box Y = 6.800 Box Z = 15.081
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 6 NFFT2 = 6 NFFT3 = 15
> Cutoff= 1.000 Tol =0.621E+00
> Ewald Coefficient = 0.35000
> Interpolation order = 4
> EXTRA_PTS: too many nghbrs!!
>
>
> If somebody knows what is wrong, please ...help me..
>
>Thanks...
>
>German
>
>

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