Hi
I am trying to do normal mode analysis on a protein with 3906 atoms, in
vacuo. I have minimized the x-ray structure using sanders to drms<1e-5. To
use nmode, I change the maxpr in nonbon1 from 2800 to 3910.
When I tried do further minimization in nmode using newton-raphson (ntrun=4) I get the
following error:
rms of step length = 0.0000000629
Bad nonbon: 1 18 0.76921E+00 0.84351E+03
Bad nonbon: 1 21 0.30746E+01 0.50627E+03
...
Bad nonbon: 1899 1914 0.29739E+01 0.54335E+02
Bad nonbon: 1899 1915 0.69180E+00 0.66862E+02
ene .step k-1 = -7952.339035 ene .k = ***************
... scaling was unsuccessful ... stop
Here's my nmode input file:
&data
ntrun = 4,
maxcyc = 200,
drms = 0.000001,
cut = 999,
idiel = 1,
scee = 1.2,
nprint = 5,
nvect = 0,
ntx = 0,
ntxo = 0,
smx = 0.01,
alpha = 0.5,
/
I've checked that the energies from the final step of sander's
minimization is the same as the first step of nmode's minimization:
-----------------------------------------------------------------
(Sanders)
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
42217 -7.9523E+03 7.8954E-06 1.2393E-04 HA 2529
BOND = 149.7237 ANGLE = 466.9506 DIHED = 2412.6363
VDWAALS = -2102.6763 EEL = -19186.0876 HBOND = 0.0000
1-4 VDW = 828.1526 1-4 EEL = 9478.9616 RESTRAINT = 0.0000
-----------------------------------------------------------------
(nmode)
step = 0
F = -0.795234E+04 GRDMAX = 0.123933E-03 GNORM = 0.789669E-05
E-NONB E-ELE E-HBOND E-BOND
-0.21027E+04 -0.19186E+05 0.00000E+00 0.14972E+03
E-ANGLE E-DIHED E-NB14 E-EEL14
0.46695E+03 0.24126E+04 0.82815E+03 0.94790E+04
E-POL E-3BOD
0.00000E+00 0.00000E+00
-----------------------------------------------------------------
I tried printing out the energies in forces.f and enb and eel are
undefined (*****)
I think that the error is due to some atom pairs being too close in
nonbon1, but I am not sure how that happen, assuming the xdir is
calculated correctly? I've stared at the code and am still baffled. any
help is appreciated!
Thanks,
Enghui
p/s: I managed to use the restart file from Sander's minimization directly for normal mode analysis (ntrun=1) and it ran ok. But I'd still like to understand why ntrun=4 did not work.
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Received on Wed Jul 16 2008 - 06:07:21 PDT
