AMBER Archive (2005)

Subject: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation.

From: zhli_2000 (zhli_2000_at_126.com)
Date: Wed Apr 20 2005 - 08:52:18 CDT

Dear Ross,
  First,I'm sorry this reply was delayed. I had thought this letter had been sent successfully on 19 Apr., but I found it didn't seem so today. So I sent this letter again.
  Thank you for advice. The following is the process to create the prmtop
and inpcrd files:
source leaprc.ff99
mod=loadamberparams FAD.frcmod
loadamberprep FAD.prep
mod=loadamberparams TEM.frcmod
loadamberprep TEM.prep
mod=loadamberparams TON.frcmod
loadamberprep TON.prep
source leaprc.gaff
RL=loadpdb ppo_cyc_4_opposite.pdb
saveamberparm RL ppo_cyc_4_o_noWT.top ppo_cyc_4_o_noWT.crd

And you will find the output files from the minimisation in the attachment.
   Thanks again.
Best wishes!
                                                   Zhli


> 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 > 79>.A
> > and .R.A
> > Warning: Close contact of 0.536569 angstroms between .R > 105>.A
> > and .R.A
> > Warning: Close contact of 0.164291 angstroms between .R > 106>.A
> > and .R.A
> > Warning: Close contact of 0.503291 angstroms between .R > 127>.A
> > and .R.A
> > Warning: Close contact of 0.157410 angstroms between .R > 177>.A
> > and .R.A
> > Warning: Close contact of 0.154235 angstroms between .R > 192>.A
> > and .R.A
> > Warning: Close contact of 0.320126 angstroms between .R > 241>.A
> > and .R.A
>
> 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
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
>
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