Dear Zhli,
> Recently,I have minimized the protein-ligand complex with two
> steps.Firstly, only hydrogens of the complex are minimized.
What process did you use to minimise the system? And how did you go about
creating your prmtop and inpcrd files, which force field etc.?
> Then minimize
> the whole system of the complex. These two steps are done
> successfully. And
> the potential energies have been converged.
We need to see the output from the minimisations to have a better idea of
what is going on please attach it to the email.
> But when I load
> the minimized
> pdb file and check it, I find some bond lengths are very
> short and are not
> reasonable. For example,
> Warning: Close contact of 0.319169 angstroms between .R<PHE
> 79>.A<HD2 18>
> and .R<GLN 200>.A<HE22 15>
> Warning: Close contact of 0.536569 angstroms between .R<ILE
> 105>.A<O 19>
> and .R<LYS 106>.A<HG3 10>
> Warning: Close contact of 0.164291 angstroms between .R<LYS
> 106>.A<HA 4>
> and .R<LYS 106>.A<N 1>
> Warning: Close contact of 0.503291 angstroms between .R<HIE
> 127>.A<ND1 9>
> and .R<HIE 412>.A<HE2 13>
> Warning: Close contact of 0.157410 angstroms between .R<ARG
> 177>.A<HA 4>
> and .R<ARG 177>.A<N 1>
> Warning: Close contact of 0.154235 angstroms between .R<NLYS
> 192>.A<HA 6>
> and .R<NLYS 192>.A<N 1>
> Warning: Close contact of 0.320126 angstroms between .R<GLU
> 241>.A<HG2 9>
> and .R<ASP 242>.A<H 2>
There is almost certainly a problem with the parameters in the prmtop file
you created which could come from a number of sources, such as problems in
your original pdb file, incorrect loading of force field parameter files
when creating the prmtop or very strange charges etc. I would double check
what you did and if you can't find a problem please email back with a much
more verbose description of what you did.
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 |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
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Received on Mon Apr 18 2005 - 18:53:01 PDT
