Re: FW: ammonia to methane/ c/o Jerome Henin

From: Jérôme Hénin (
Date: Fri Apr 23 2010 - 10:57:05 CDT

Hi Dale,

The CH4.pdb file has incorrect formatting (even more so than the
ammonia one, since it is missing the chain identifier). You could just
open and save it with VMD to improve this. And there is a problem with
aliasing the atom name: CB is aliased to CT3 instead of the opposite
(the simplest way here would be to give atoms and residues consistent
names and not do any aliasing).


On 23 April 2010 17:19, Dale l. Schruben <> wrote:
> The attached files (methane) that do not work where hacked together my me from the ammonia files.  There are fields therein that are not covered in the tutorials, hence my hack.  Any suggestions to get psfCH4.pgn running correctly would be appreciated.  Dale
> ________________________________
> From: Dale l. Schruben
> Sent: Wed 4/7/2010 11:37 AM
> To:
> Subject: ammonia to methane
> The attached files to run psfNH3.pgn were given to me and work.  The parallel files to run psfCH4.pgn run imperfectly?
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