Hello Amber users,
I am trying to use Amber 7 with GO like model (not using Amber force
field) I found that when NPHB - number of distinct 10-12 hydrogen bond
pair types is larger than 500, Amber does not run and produces multiple
errors when all the other parameters to a simulation are kept the
same(it runs OK if this number is less than 500, and all of the
parameters that are read as stars are read in normally then), here is
the output I get if NPHB> 500 (pasted below).
I also have another question unrelated to the simulation mentioned
above: If I have let's say NTYPES = 20, NPHB = 210 and specify LJ10-12
energies (not using Amber's force field) for all 210 possible
interactions, in what section of the prmtop file should I indicate the
types of "atoms" I have in my protein: is it ISYMBL(i) - the Amber atom
types for each atom? Is there also a way to exclude energy calculation
if i and j are separated by fewer than 3 residues (this is what I was
trying to do in the first part - question 1, and therefore represent
every "atom/residue" in my protein as a separate "atom type" => NPHB
becomes > 500)?
Thank you, any help is greatly appreciated,
Alena
PhD Student
University of British Columbia
Vancouver, Canada
-------------------------------------------------------
Amber 6 SANDER_CLASSIC Scripps/UCSF 1999
-------------------------------------------------------
| Sat Nov 27 13:16:52 2004
[-O]verwriting output
File Assignments:
|MDIN :
minimd.400.52831.in_pre
|MDOUT:
pre_out.400.52831
|INPCR:
prm.crd
|PARM :
prmtop
|RESTR:
restrt.400.52831
|REFC :
refc
|MDVEL:
mdvel
|MDEN :
mden
|MDCRD:
mdcrd
|MDINF:
mdinfo
Here is the input file:
#
# input file for SANDER ( MD
)
# 1 1 1 1 1 1
1
&cntrl
timlim = 999999. , irest = 0, ibelly = 0, kform = 1, ichdna =
1,
imin = 0,ntx = 1,ntxo = 1,ig = 52831,tempi
=400,
heat = 0.0,ntb = 0,iftres = 1,nrun = 1,ntt = 5,temp0 =
400,
dtemp =
25.,
iewald =
0,
tautp = 0.2,tauts = 0.2,ntp = 0,pres0 = 1.0,comp = 44.6,taup =
0.2,
npscal = 0,ndfmin = 0,ntcm = 1,nscm = 1000,nstlim = 100000,init =
3,
ntu = 1,t = 0.0,dt = 0.005,ntc = 1,tol = 0.0005,ntf = 1,ntid =
0,
ntnb = 1,nsnb = 99999,idiel = 1,imgslt = 0,cut = 1000.0,scee =
1.2,
dielc = 1.0,ntpr = 400,ntwx = 400,ntwv = 0,ntwe = 400,ntwxm =
0,
ntwvm = 0,ntwem = 0,ioutfm = 0,ntr = 0,ntrx = 1,scnb =
10000.,
taur = 0., nmrmax = 0, isftrp = 0, rwell = 0., pencut =
..01,
ivcap = 0,fcap =
0.0,
maxcyc = 50,ncyc = 10,ntmin = 1,dx0 = 0.01,dxm = 0.5,dele =
0.0001,
drms =
0.0001
&end
&wt type='END'
&end
-------------------------------------------------------------------------------
#
| Reading &cntrl namelist w/ machine lib
1. RESOURCE USE:
NATOM = 37 NTYPES = 37 NBONH = 0 MBONA = 36
NTHETH = 0 MTHETA = 35 NPHIH = 0 MPHIA = 34
NHPARM = 0 NPARM = 0 NNB = 106 NRES = 37
NBONA = 36 NTHETA = 35 NPHIA = 34 NUMBND = 36
NUMANG = 35 NPTRA = 68 NATYP = 37 NPHB = 550
IFBOX = 0 NMXRS = 1 IFCAP = 0
| Memory Use Allocated Used
| Real 13000000 1367
| Hollerith 2000000 335
| Integer 9000000 1002414 (static)
| Max Nonbonded Pairs:40000000 packed 2 to a machine word
2. CONTROL DATA FOR THE RUN
TITLE
TIMLIM= 999999. IREST =***** IBELLY= 0
KFORM = 1 ICHDNA= 1 IMIN =*****
IPOL = 0 IEWALD= 0
NTX =***** NTXO =*****
IG =********* TEMPI = 400.00 HEAT = 0.000
NTB =***** IFTRES=***** BOXX = 0.000
BOXY = 0.000 BOXZ = 0.000
NRUN =***** NTT =***** TEMP0 = 400.000
DTEMP = 25.000 TAUTP = 0.200 TAUTS = 0.200
ISOLVP=***** VLIMIT= 0.000
NTP =***** PRES0 = 1.000 COMP = 44.600
TAUP = 0.200 NPSCAL=*****
NTCM =***** NSCM =********
NSTLIM=***** INIT = 4 NTU =*****
T = 0.000 DT = 0.00500
NTC =***** TOL = 0.00050 JFASTW =*****
NTF =***** NTID =***** NTNB =*****
NSNB =***** IDIEL =***** IMGSLT=*****
IPRR = 0 IPRW = 0 ITRSLU=*****
CUT = 1000.000 SCNB =10000.000
SCEE = 1.200 DIELC = 1.000
CUT2ND= 0.00000
NTPR = 400 NTWR = 50 NTWX = 400
NTWV = 0 NTWE = 400 NTWXM = 0
NTWVM = 0 NTWEM = 0 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0
NTR =***** NTRX =*****
TAUR = 0.00000 NMROPT= 0 ISFTRP=*****
RWELL = 0.00000 PENCUT= 0.01000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
IRDARC= 0 IRD1ST= 0 IRDLST= 0
IWRTSM= 0
OTHER DATA:
IFCAP =***** NATCAP=***** CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
NATOM = 37 NRES = 37
MAXCYC=***** NCYC =***** NTMIN =***** DX0 =
0.010000
DXM = 0.50000 DRMS = 0.00010
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name =
H2
GFTIM = 2.00000 RLMAVF= 0.00000 ISGDEP= 3
NMRAFA= 0 ILTAVF= 0
IREST (***) must be 0 or 1.
NTX (***) must be in 1..7
NTXO (***) must be 1 or 0.
NTB (***) must be 0, 1 or 2.
IFTRES (***) must be 0 or 1.
NTT (***) must be <=5.
NTP (***) must be 0, 1 or 2.
NPSCAL (***) must be 1 or 0.
NTCM (***) must be 0 or 1.
%SANDER-W-KCAL, Amber uses only Kcal/mol units
NTU (***) reset to 1.
NTC (***) must be 1,2,3 or 4.
JFASTW (***) must be 0->4.
NTF (***) must be in 1..8.
NTID (***) must be 0 or 86.
NTNB (***) must be 1 or 0.
IDIEL (***) must be 0 or 1.
IMGSLT (***) must be 0 or 1.
ITRSLU (***) must be 1 or 2.
NTR (***) must be 0 or 1.
NTRX (***) must be 1 or 0.
NTP > 0 but not constant pressure P.B.C. (NTB = 2) must be used
CUT must be < half smallest box dimension
*** input error(s)
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Received on Sat Nov 27 2004 - 22:53:00 PST
