Re: [AMBER] CHAMBER: error in finding bond type

From: Mark Williamson <>
Date: Tue, 16 Oct 2012 13:24:38 +0100

On 16/10/12 12:28, Mike Limb wrote:
> Dear Amber users,
> I am currently trying to use CHAMBER in order to convert my CHARMM
> compatible files to use in AMBER.
> My system contains is solvated with explicit solvent and contains a signal
> chain enzyme and a ligand (for which I have custom developed CHARMM
> parameters).
> I use the command:
> chamber -cmap -top nag_nam_protein_top_CMAP.inp -param
> par_sugar_protein_chamber.inp -psf hewl_mgm1_solv_charmm.psf -crd
> ionized.pdb -p hewl_sugar.prmtop -inpcrd hewl_sugar.inpcrd

Dear Mike,

Can you send me your all your inputs, off list, in a tar.bz2 file and
I'll try to debug it.

CHAMBER has a slightly relaxed input parser (look in the psf_strings
module) that does not actually use s specific format string (e.g.
I5XF10.3) in the Fortran read() subroutine. Most of the bugs in CHAMBER
are generally due to some latent deviation in the expected formatting,
in the inputs (i.e. a stray tab will break it). The result of this, is
that the problem is not caught during the input phase, instead
percolates through the code and results in quite an esoteric error, far
from the original cause.

(To) Mike Crowley, your local parsing changes we spoke of, off list, a
few months ago, did they ever make it into the main tree? Mysteriously,
I've not got write access, hence you may need to push them, rather than
supplying a patch file to me.



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Received on Tue Oct 16 2012 - 10:30:05 PDT
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