Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP

From: Mark Williamson <>
Date: Tue, 30 Oct 2012 11:48:27 +0000

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.



Mark J. Williamson
Unilever Centre for Molecular Informatics
Department of Chemistry
Lensfield Road
Cambridge CB2 1EW
AMBER mailing list
Received on Tue Oct 30 2012 - 05:00:02 PDT
Custom Search