Hi Charles,
Yes, you are right!I If All PRE related terms are taken out, the script can
be finished, except: tmsp in checkAndCorrect is too small and I changed it
from 1.0e-4 to 1.0e-6 to make program go through this error. How can I fix
the problem about these PREs? Thanks a lot!!
Best wishes,
Jie-rong
2008/4/22, Charles at schwieters.org <Charles at schwieters.org>:
>
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>
> Hello Jie-rong--
>
> >
>
> > Some error messages at the first begining of terminal window that I
> didn't
> > notice last time:
> > ############
> > calcD_G: singular D matrix: { { nan } }
> > H matrix: { { nan, nan, nan, 0, 0, 0 } }
> > node level: 227
> > number of children: 0
> > atoms:
> > 1228 GLY 76 C : { nan, nan, nan }
> > 1229 GLY 76 OT1 : { nan, nan, nan }
> > 1230 GLY 76 OT2 : { nan, nan, nan }
> > ############
> > Is this the second possibility you mentioned?
>
>
> The NANs confirm that the gradient is the problem. You will need to
> figure out which potential term is causing these by disabling terms one
> by one.
>
>
> >
> > The pdb and psf files input are both:
> > ############
> > ATOM 1229 C GLY 76 127.034 0.640 -0.873 1.00 1.00
> > ATOM 1230 OT1 GLY 76 127.291 -0.478 -1.288 1.00 1.00
> > ATOM 1231 OT2 GLY 76 127.580 1.657 -1.268 1.00 1.00
> > ############
> > ############
> > 1229 76 GLY C C 0.140000 12.0110 0
> > 1230 76 GLY OT1 OC -0.570000 15.9990 0
> > 1231 76 GLY OT2 OC -0.570000 15.9990 0
> > ############
> > The atom numbers are inconsistent with those indicated in error message,
> is
> > it the problem?
> >
>
>
> no. Atom numbers differ between the C++ and Fortran code.
>
>
> best regards--
> Charles
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