Re: AMBER: peoblemwith RED II

From: FyD <>
Date: Sat, 28 Aug 2004 11:52:20 +0200


> As you had advised me earlier, I splited my structure into 2 parts to
> calculate the RESP charges. For this first I used AM1 method for
> convergence and then I shifted over to 6 31G* method. Meanwhile ZI
> proceeded from the AM 1 minimized structure, just to check the prpotocl It
> worked fine. But the process I ran using 6 31 G* has still not converged.
> the nstep value is 213 and the gradients are as follows:
> MAXIMUM GRADIENT = 0.0000873 RMS GRADIENT = 0.0000339
> Whys is the structure still taking so long to comverge?

This means your AM1 structure is quite different from your 6-31G* one. I guess.

- You could try to use your AM1 structure as input for 3-21G
and then the 3-21G structure as input for 6-31G* ?

- You could try to calculate the Hessian every 10 steps as I already told you.

- I am not surprised by your problem because if you do not have a powerfull
computer (i.e. a cluster) it might take a while to get a 6-31G* opt.

> Another question which I want to ask is as follows:
> As you know my system consists of 2 parts an amino acid (lys) and an
> organic molecule. Now when I calculate the RSP charges for this, should
> the charges calculated for the lys portion be similar to the ones that are
> used in amber and if yes then how much is the permicible difference?

I would say yes... However what does it mean 'similar' ?
I would say, you should not observe a max. difference of 0.07 e or max. 0.1 e
(because of additional restraints in your case)...
If you get something higher than that you have a problem somewhere (i.e. RESP

> the
> organic molecule is bound to lys and i have splitted the system into lys
> and organic molecule both protected by end groups.

Such branched molecule seems OK to me.


F.-Y. Dupradeau
Faculte de Pharmacie, UPJV, Amiens, France
The Scripps Research Institute, San Diego, USA
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Received on Thu Sep 02 2004 - 01:15:11 PDT
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