AMBER Archive (2009)

Subject: Re: [AMBER] Re: COOH troubling

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Dec 10 2009 - 15:45:43 CST

Hi,
I have carefully examined your molecule. The structure should be correct
(forming C=O, neutral). I am not sure how you did QM calculations and how
you set the radii for Iodine. I calculated HF/CEP-121G (the radii for I was
set to 1.98) optimization for your ligand molecule and derived the resp
charges. I can see the difference between yours and mine is enormous. Please
see the attached prepi file.

After that, I tried to repeat your MD results. Using your charges, the 1-4
interaction became unrealistic negative and led the program to crash for
both minimization and MD. However, with my RESP charges based on HF/CEP-121G
(I think HF/CEP-31G, which mimics the HF/6-31G* better, should be used), the
minimization and MD were run smoothly. Please see the attached sander
outputs.

According to my experience, gaff can handle most organic molecules well and
I have successfully run MD simulations for at least 500 organic molecules,
all in TIP3P water or the other organic solvents. The trouble molecules I
met are those containing high positive or negative charges (>1.5 and < -1.5)
or those are gases at the simulation contidions. For most trouble molecules,
I still can make MD running by modifing MD inputs and minimizing the unideal
strctures.

Good luck

Junmei

On Thu, Dec 10, 2009 at 5:03 AM, Jio M <jiomm_at_yahoo.com> wrote:

> Dear Dr. Dean and J. Wang;
>
>
>
> >Either get rid of the double bond and add a negative charge to make a
>
> phenolate ion, or make a C-O-H by adding a hydrogen to the oxygen to make a
>
> phenolic group, like you have on the opposite side of your anthracene ring
>
> system.
>
>
>
> I am sending link which shows my structure.
>
> http://www.wag.caltech.edu/publications/sup/pdf/370.pdf
>
> But I have used RESP charges. There some other charge method is used. I
> think it is C double bond O.
>
>
>
> thanks and regards;
>
> JIomm
>
>
>
>
>
>
>
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>


  • application/octet-stream attachment: lig.prepi

  • application/octet-stream attachment: lig2.mol2

  • application/octet-stream attachment: min6.out

  • application/octet-stream attachment: md7.out

  • chemical/x-pdb attachment: md7.pdb

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