Re: [AMBER] Re: COOH troubling

From: Jio M <>
Date: Fri, 11 Dec 2009 22:27:25 -0800 (PST)

>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


I used this for lig.mol2 that I provided as attached file: 
hf/lanl2dz SCF=Tight Pop=MK IOp(6/33=2,6/41=10,6/42=17)
geom=connectivity pop=(mk,readrad)

Iodine radius also set to 1.98 Angstrom and derived RESP with antechamber.

The attached lig2.mol2  was having charges provided by your method
HF/CEP-121G (pls correct me if I am wrong). I was able to run dynamics
not only of single ligand but also in docked state by loading your
lig2.mol2 file. But I did parmchk on lig2.mol2 to get frcmod file. I
used .in file as given in min6.out and md7.out.

But when I use my conditions, same thing happened , COOH trouble and
ring distortion.Using my conditions even single molecule dynamics is

this is input file:


  imin = 0,

  ntb = 2, pres0 = 1.0, ntp = 1,

  taup = 2.0,

  cut = 8.0, ntr = 0,

  tempi = 0.0, temp0 = 0.0,

  ntt = 3, gamma_ln = 1.0,

  nstlim = 100000, dt = 0.0001,

  ntpr = 100, ntwx = 100, ntwr = 1000


But by USING your input file and charges I was succesfull always.

It would add to my knowledge if you can please share how to decide and
become confident that HF/CEP-121G or other basis will fit. Does it
depends on relative RMS SQRT while doing RESP calculations.

One problem still hanging, in starting few trajectories I can see that
COOH group is cis but after some ps it becomes trans. Does the force
constant of CO--OH bond rotation is weaker.

>You also need to question why the article used the protonated carboxyl and

>protonated phenolic form.

I checked cross ref. of the experimental procedure they are following
to simulate. The release pattern was studied by dialysis with solvents
which I think donot have pH of 2. there is no clear cut pH conditions
mentioned. May be I am still missing something to understand why
protonated structure was used.

>You need to seriously consider the pH at which you want to
simulate, because that will >completely determine which of the three
protonation forms you need to parameterize

Yes, honestly, I was not so much serious before, regarding such
structures. Now I will consider the things. Thanks for giving such a
detailed information for my ligand.

>Good luck with your work,

I am highly thankfull to Dr. Dean, Dr. Case and Dr. Junmei, for the explanation

thanks and regards;


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Received on Fri Dec 11 2009 - 22:30:03 PST
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