Dear Dr. Mark,
Thank you for your great help. It works well now.
Best wishes,
Duan Baogen
2012/10/30 Mark Williamson <mjw.mjw.name>
> On 25/10/12 06:19, duanbg wrote:
> > Dear Dr. Mark,
> >
> > I am sorry to interrupt you. Recently, I want to use
> chamber program in AmberTools 1.5 to convert charmm psf file to Amber top
> and crd file. And I met the problem when dealing with DNA, RNA and ATP
> molecules, it gives error message which is " Bad value during floating
> point read (line 847 of file _psfprm.f )" in dealing with dihedral parts.
> But for the protein, the conversion is OK. And a single residue of DNA is
> also OK.
> >
> > I looked for the Amber forum and found the same problem when
> dealing with RNA molecule. But the solution for this problem is not shown.
> So, I am writing to you to hope to help me with this problem. Thank you in
> advance.
> >
> > the command I used is :
> > chamber \
> > -top top_all27_prot_na_mod.inp \
> > -param par_all27_prot_na.prm\
> > -psf gua.psf -nocmap\
> > -crd gua.pdb \
> > -p prmtop \
> > -inpcrd inpcrd -verbose
> > and the corresponding files are enclosed.
> >
> > Best wishes
> > Yours Sincerely,
> >
> > Duan Baogen
> >
>
>
> Dear Duan,
>
> I'm replying also to the list with this one, since I've seen the same
> issue with this specific dihedral parameter line once already this week.
> On line 3198 in your par_all27_prot_na.prm:
>
> HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5'
>
> there is a tab character after 0.195. This is tripping up CHAMBER's
> basic parsing ability; removing it should fix the issue. Purported fixes
> to catch this have yet to materialise into the tree.
>
> Regards,
>
> Mark
>
> --
> Mark J. Williamson
> Unilever Centre for Molecular Informatics
> Department of Chemistry
> Lensfield Road
> Cambridge CB2 1EW
>
> http://www-ucc.ch.cam.ac.uk/members/mw529
>
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Received on Wed Oct 31 2012 - 20:00:04 PDT
