AMBER Archive (2004)

Subject: Re: AMBER: RED fails to read g94 output

From: FyD (
Date: Sat Aug 14 2004 - 03:26:33 CDT

> I used the "JOB1-gau.log" file as minimization
> output but RED exited saying that the minimization output is not valid.
> This is a huge problem because I dont want to do the optimization again.
> Did someboday experience this problems before? If yes could somebody
> help me with this?

and check carefully that each atom name in the starting PDB name is composed of
the 'chemical symbol' + 'T' (if needed) + 'a number'. This affects the
minimisation ouput recognition...

i. e. avoid atom names such as O4', 1H1 or HO1
O4' should be replaced by O4 (for instance)
1H2 by H2 (for instance)
HO1 by H1 (for instance)
This has been really din the R.E.D. version II which will be released beginning
of september. F.
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