AMBER Archive (2004)

Subject: Re: AMBER: Problems with X.R.E.D.

From: FyD (
Date: Fri Jun 25 2004 - 12:20:30 CDT

Hi Scott,

> I am new to working with R.E.D. and I am looking for some assistance
> from the group. I recently set up a simulation to run the sequence
> LEU NME using six orientations on R.E.D (using the GAMESS package). I
> was looking for resp charges and used the pdb minimization options.
> Everything seemed to go well however it never finished the
> minimization
> of the pdb file. I finally terminated the project after seven days
> after giving up hope that it would finish minimization (the log file
> was
> appended to every few minutes and grew to the size of 5 Mb at the end
> of
> the seven days). Has anyone had any experience like this before? If
> this is normal, how can I tell when the minimization should be
> completing?

If I understand you, your problem is not with using X R.E.D. but using GAMESS...

Several points:

- When you have a big optimization job, I think it is better to run minimization
without R.E.D. and once you got the minimum (using different min. input tests),
to run R.E.D. with the following variables:
$OPT_Calc = "Off";
$MEPCHR_Calc = "On";
$MOL_START = "./Your_PDBFile.pdb";
$JOB_OPT = "./Your_Path/Your_GAMESSminimization_out.log";

- I am not surprised it takes so long because we strongly decreased the
minimization thresholds in GAMESS minimization in order to get similar results
than Gaussian i.e. we used the following keywords:
          QMTTOL=1.0E-08 ITOL=30 ICUT=20 $END
 $SCF CONV=1.0E-08 $END
Thus it may not be very 'convenient' in particular if you do not use a cluster
of computers.

- Now if I look at your GAMESS ouput, you get:
> MAXIMUM GRADIENT = 0.0000827 RMS GRADIENT = 0.0000318

This means your structure is ~ correct but its accuracy is not enough to insure
reproducible charges.

- What can you do? I would try 2 things:
* 1st starts from the structure which presents the MAXIMUM GRADIENT = 0.0000827
and continue the minimization but calculating its hessians. See manual RED.pdf
page 12 using: the $STATPT and $FORCE groups calculating the hessian every 10
structures (for instance). The Hessian calc. will take time but should allows
you to reach the minimum in less minimization steps.
* If you still cannot get the minimum, you could start to decrease the GAMESS
minimization thresholds i.e. remove from the min. input:
and if it is still not enough use:

However, I would not recommand to decrease the minimization thresholds (in
particular I would keep OPTTOL=1.0E-06) because your charges might not be
reproducible with this new input (OPTTOL=1.0E-05)...

Regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
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