Dear Zhli,
> VDWAALS = 3737761.5360 EEL = -29654.0849 HBOND =
0.0000
Your initial van der Waals term is huge. This suggests that there is a
problem with your starting structure. You most likely have two atoms almost
on top of each other. The minimiser can often cleanup bad structures but in
your case some atoms are likely very close together and so it gets trapped
in a local minima. One where it shortens bonds to unreasonable lengths in
order to relieve huge VDW strains.
I would check your starting structure carefully and see if you can find out
where the problem is. If it isn't easy to spot try running a few steps of MD
with a short time step, say 0.5fs and writing to the mdcrd file every step
ntwx=1. You can then visualise this in something like VMD and see where you
system rapidly blows up from. This will give you a region to look. You can
also try the check command in leap which should report any close contacts.
Look for things of less than 0.8 angstroms or so.
If you can't find anything wrong with your structure then double check the
non bonding parameters you are using. Also verify that your amber mpi
installation passes the test cases just in case.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Apr 20 2005 - 18:53:00 PDT
