|
|||||||||||||||||||||||||||||||||
AMBER Archive (2009)Subject: Re: [AMBER] Re: COOH troubling
From: Jio M (jiomm_at_yahoo.com)
>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 used this for lig.mol2 that I provided as attached file:
Iodine radius also set to 1.98 Angstrom and derived RESP with antechamber.
The attached lig2.mol2 was having charges provided by your method
But when I use my conditions, same thing happened , COOH trouble and
this is input file:
&cntrl
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
One problem still hanging, in starting few trajectories I can see that
>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
>You need to seriously consider the pH at which you want to
Yes, honestly, I was not so much serious before, regarding such
>Good luck with your work,
I am highly thankfull to Dr. Dean, Dr. Case and Dr. Junmei, for the explanation
thanks and regards;
JIomm
| |||||||||||||||||||||||||||||||||
|