Dear amber community
I am using nmode to do Newton-Raphson minimisation
The input protein is obtained from PDB, H atoms removed, then processed with
tleap to get the prmtop & inpcrd files.
However, the NR minimisation get terminated early and I am not sure how to
troubleshoot this.
Any suggestions?
Many thanks!
=====================
The input nmdin file:
&data
ntrun=4,
nsave=2,
ndiag=2,
cut=95.0,
nprint=100,
drms=0.00001,
maxcyc=100,
bdwnhl=0.01,
dfpred=0.1,
scnb=2.0,
scee=2.0,
nvect=200,
ntxo=1,
&end
================
The nmdout file:
minimization for
nmode
ntrun maxcyc ibelly drms
4 100 0 0.10E-04
rcut scnb scee dielc idiel
95.00000 2.00000 2.00000 1.00000 0
nsave dfpred bdwnhl smx emx alpha ndiag
2 0.10000 0.01000 0.08000 0.30000 0.80000 2
ipol = 0
i3bod = 0
nvect = 200
| New format PARM file being parsed.
| Version = 1.000 Date = 03/20/08 Time = 15:42:26
PARM file has the title:
Total memory required : 301034923 real words
Total memory required : 17074060 integer words
Total memory required : 17712 4-character words
Maximum nonbond pairs 16701309
Duplicated 0 dihedrals
Duplicated 0 dihedrals
Getting coordinates from file with title:
Number of non-bonded pairs = 16669620
Number of H-bonded pairs = 0
***************** ***************** *****************
step = 0
F = 0.153216E+06 GRDMAX = 0.177166E+07 GNORM = 0.219344E+05
E-NONB E-ELE E-HBOND E-BOND
0.15252E+06 -0.80776E+04 0.00000E+00 0.17805E+03
E-ANGLE E-DIHED E-NB14 E-EEL14
0.82970E+03 0.35161E+04 0.18596E+04 0.23887E+04
E-POL E-3BOD
0.00000E+00 0.00000E+00
Coordinate origin is now the molecular center of mass
b1 = ********** b2 =********** tlamba = **********
rms of step length = ************
Stop in nonbon1, npr= 5767
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Received on Fri Apr 18 2008 - 21:15:38 PDT
