AMBER Archive (2004)

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

From: FyD (
Date: Sat Aug 14 2004 - 00:34:21 CDT

> I am dealing with RED for the first time and I would appreciate a
> little help. I did manage to do an optimization (the question if
> Opt=Tight and Conver=8 are required is still unanswered)

I just answered to your last email. I will not be able to read my email very
often until beginning of september...

> but after the
> optimization RED exited with the message below. I figured out that this
> might be the same as the bug no.1 report so I changed the code
> accordingly.

To use gaussian 94 ouput : see the bug 1 report.

> Then i tried to run RED but only for the charge calculation
> with optimizing again. I used the "JOB1-gau.log" file as minimization
> output but RED exited saying that the minimization output is not valid.

Several thing:
- The atom order in your starting PDB file and QM output must be THE SAME
- Your QM ouput must contains three set of words:
1) 'Normal termination of Gaussian' at the end
2) 'Stationary point found' located BEFORE a
3) 'Standard orientation'

I know sometimes the 'Standard orientation' is not printed in the gaussian
ouput... In this case, use the .chk file to run a single point to re-generate
an optimized 'Standard orientation'. Add the words 'Stationary point found'
located before this 'Standard orientation' and it should be OK...

Regards, Francois

Before using R.E.D. on your molecule, read the manual in detail and try to get
charges using a small molecule reported in the tutorial. EtOH is a good example
because very simple. Once you did a lot of tests and learnt how to use R.E.D.
with EtOH or MeNH2 then use your molecule...

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