Dear All,
I have some basic questions about thermodynamics integration, I am
trying to build a system where N2 is being replaced with C0, i.e
Nitrogen is being replaced with Carbon atom.
I am following the all instructions as given in tutorial A 9 and have
created the .prm and .rst files. Now when I am trying to run a
conversion of N2 to C0 with soft core I can easily run the group file
whic contains the minimization instructions with lambda 0.5, but I am
unable to run the equilibrium group file with lambda 0.5 . Here is how
I am getting an error as shown below. I have google about this error
and search the mailing list but did not find any solution. In the
group file both process have same number of atoms (this process:
69813 atoms, partner process: 69813 atoms)
Please help me to fix this issue. I am not sure what I have to change
in the input files. My starting PDB files are both same except this N2
and C0 of the ligand.
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 04/01/2010 at 13:48:44
[-O]verwriting output
File Assignments:
| MDIN: mdin_equi_v0_l5
| MDOUT: prot_imt_equi_v0_l5.out
|INPCRD: prot_imt_min_v0_l5.rst
| PARM: prot_imt.prm
|RESTRT: prot_imt_equi_v0_l5.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
density equilibration
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 2500, ntwr = 10000, ntwx = 0,
ntf = 1, ntc = 2,
ntb = 2, cut = 9.0,
nstlim = 25000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
icfe=1, clambda = 0.5,
ifsc=1,
crgmask=':IMT.N2',
scmask=':IMT.N2',
&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 = 39.392
| New format PARM file being parsed.
| Version = 1.000 Date = 04/01/10 Time = 13:14:21
NATOM = 69813 NTYPES = 18 NBONH = 51157 MBONA = 18717
NTHETH = 5609 MTHETA = 3378 NPHIH = 10578 MPHIA = 7824
NHPARM = 0 NPARM = 0 NNB = 140763 NRES = 16536
NBONA = 18717 NTHETA = 3378 NPHIA = 7824 NUMBND = 59
NUMANG = 117 NPTRA = 53 NATYP = 42 NPHB = 1
IFBOX = 1 NMXRS = 32 IFCAP = 0 NEXTRA = 16232
NCOPY = 0
| Memory Use Allocated
| Real 3743046
| Hollerith 435416
| Integer 2174078
| Max Pairs 37168441
| nblistReal 837756
| nblist Int 3019125
| Total 202963 kbytes
| 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 = 2500, ntrx = 1, ntwr = 10000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 25000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Extra-points options:
frameon = 1, chngmask= 1
Free energy options:
icfe = 1, ifsc = 1
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 = 78.784 Box Y = 93.096 Box Z = 88.756
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 96 NFFT3 = 90
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
Zero-Charge Mask :IMT.N2; matches 1 atoms
Removing charge of 0.1307 from atom 4860
Total charge of 0.1307 removed
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 51157 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 51157 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 18717 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 2485 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 5609 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 5609 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 3378 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 3378 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 10578 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 10578 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 7824 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 7824 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 16232
| Atom division among processors:
| 0 69813
Softcore Mask :IMT.N2; matches 1 atoms
this run corresponds to V0, its softcore atoms interact fully for lambda=0
this process: 69813 atoms, partner process: 69813 atoms
Checking for mismatched coordinates.
WARNING: Local coordinate 14572 differs from partner coordinate 14572 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14573 differs from partner coordinate 14573 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14574 differs from partner coordinate 14574 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14575 differs from partner coordinate 14578 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14576 differs from partner coordinate 14579 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14577 differs from partner coordinate 14580 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14623 differs from partner coordinate 14623 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14624 differs from partner coordinate 14624 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14625 differs from partner coordinate 14625 !
Deviation is small, changing partner coordinate.
WARNING: Local coordinate 14626 differs from partner coordinate 14626 !
SANDER BOMB in subroutine sc_check_and_adjust
Atom coordinate disagreement
Check input files.
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Received on Thu Apr 01 2010 - 06:30:05 PDT
