Dear Pawel,
> After minimization I get BOND=***** but amber menaged to write the
> coordinates. I visualized it. It seems like a huge force make two
> atoms bond very large. The bond is even as large as protein. Could
> it be my mistake or is it amber making it? I don't know what is
> happening.
What does the initial structure look like, Load it by using the parmtop and
the inpcrd file so that you see the real bonding rather than a pdb which is
often just bonded by distance. Do you have any atoms that are very close
together? What does the very first step of minimisation report, is anything
very high here, particularly the VDW, 1-4VDW, EEL and 1-4EEL?
Also what are you using for your parameters, especially for the ligand. Are
these okay? Try running the ligand on its own and the protein on its own.
This might uncover any problems with your parameters.
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 Fri Aug 26 2005 - 16:53:03 PDT
