AMBER Archive (2004)

Subject: Re: AMBER: resp error message

From: Andre Farias de Moura (andre_at_qt.dq.ufscar.br)
Date: Thu Sep 30 2004 - 08:58:38 CDT

hi Francois,

I've tried both suggestions and got the same error message as before:

 chgopt: LU decomp gave almost-singular U

I just set all the atoms as independent from each other (ivary=0) and
tested two different orientations but it didn't work.

any other suggestion?

thanks again,

andre'

On Wed, 29 Sep 2004, FyD wrote:

> > in fact I used XRED to do the resp fitting. I defined
> > only one orientation in my reference pdb file:
> >
> > REMARK REORIENT 38 71 73
> > REMARK
> > ATOM 1 CT1 PPEEB 20.926 9.330 13.547 1.00 0.00 C
> > ATOM 2 H1 PPEEB 21.879 9.323 14.073 1.00 0.00 H
> > ATOM 3 H1 PPEEB 20.982 10.018 12.704 1.00 0.00 H
> > ATOM 4 H1 PPEEB 20.138 9.652 14.227 1.00 0.00 H
> > ATOM 5 CT2 PPEEB 20.631 7.995 13.063 1.00 0.00 C
> > ATOM 6 H2 PPEEB 20.576 7.308 13.906 1.00 0.00 H
> > ATOM 7 H2 PPEEB 21.419 7.674 12.383 1.00 0.00 H
> > ATOM 8 CT2 PPEEB 19.362 8.005 12.362 1.00 0.00 C
> > ...
> >
> > as to the number of restraints, I defined them in the pdb file, which
> > RED used to generate input1, but I don't think there were too many,
> > they were only 4 oxygen atoms out of 112 atoms. I also tried to write
> > my own input file to run the resp program. I tried to fix the charges
> > of aliphatic atoms to their typical values while the aromatic moiety
> > charges were optimized, but then I got 'nan' message for all the
> > unconstrained atomic charges.
> >
> > can you figure out what could be wrong?
>
> - Try in a first step without any restraint, i.e. using:
>
> ATOM 1 C1 PPEEB 20.926 9.330 13.547 1.00 0.00 C
> ATOM 2 H2 PPEEB 21.879 9.323 14.073 1.00 0.00 H
> ATOM 3 H3 PPEEB 20.982 10.018 12.704 1.00 0.00 H
> ATOM 4 H4 PPEEB 20.138 9.652 14.227 1.00 0.00 H
> ATOM 5 C5 PPEEB 20.631 7.995 13.063 1.00 0.00 C
> ATOM 6 H6 PPEEB 20.576 7.308 13.906 1.00 0.00 H
> ATOM 7 H7 PPEEB 21.419 7.674 12.383 1.00 0.00 H
> ATOM 8 C8 PPEEB 19.362 8.005 12.362 1.00 0.00 C
>
> - Try another mol. orientation to see if with a different MEP you get the same
> problem...
>
> Francois
>
> PS: Please tell me what you get...
>
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