Sorry for multiple emails, but I want to make it clear.
I first tried to use the RESP charges obtained with the iop(6/33=2)
iop(6/42=6) iop(6/50=1) keywords ("automated way"). The absolute values of
those charges seems to be to high, and when I used them, the bond lengths
between the central carbon and the nitrogens are 0.06 Å shorter than the
reference value or the bond length obtained by a quantum calculation
Then I tried to use the RESP charges obtained with the iop(6/50=1) keyword
only, which seem to be "well balanced" with the gaff and ff12SB forcefields
(for example the charges of the arginine guanidinium group). It's still
impossible to parametrize the molecule (the bond lengths are still more
than 0.02 Å shorter, and I get other problems with angles).
The absolute values of the am1-bcc charges seem very low in comparison with
the arginine guanidinium, but I can get a reasonable equilibrium geometry
with them.
It seems that I have to choose between a good geometry and well balanced
charges... What's the best choice?!
*Jérémie Knoops*
*PhD StudentLaboratory for Chemistry of Novel Materials
<
http://morris.umh.ac.be/default.aspx>*
*University of Mons <
http://portail.umons.ac.be/en2/>*
2015-11-02 10:06 GMT+01:00 Jérémie Knoops <jeremie.knoops.gmail.com>:
> Hi,
>
> The antechamber "automated way" to determine RESP charges, as reported
> here: http://www.ub.edu/cbdd/?q=content/gaussian-09-and-antechamber12 ;
> create gaussian input files with the following keywords: iop(6/33=2)
> iop(6/42=6) iop(6/50=1).
>
> But it seems that using iop(6/50=1) only is a better way to get well
> balanced charges for the amber & gaff forcefields.For example, only this
> keyword is mentionned In the gaussian manual (
> http://www.gaussian.com/g_tech/g_ur/k_population.htm ).
>
> Why are those extra keywords iop(6/33=2) & iop(6/42=6) added in
> the automated way?
>
>
> *Jérémie Knoops*
>
> *PhD StudentLaboratory for Chemistry of Novel Materials
> <http://morris.umh.ac.be/default.aspx>*
> *University of Mons* <http://portail.umons.ac.be/en2/>
>
>
> 2015-10-27 11:02 GMT+01:00 Ye Mei <ymei.itcs.ecnu.edu.cn>:
>
>> RESP charge fitting suffers from ill-conditioning of the linear equations,
>> which means that you may get "degenerate" solutions for the atomic
>> charges.
>> Some might be unphysical.
>> Usually, AM1 charges are fine. Or I should say they are compatible with
>> existing AMBER force fields.
>> If you REALLY want to use ESP-based charge, you can use our dRESP charge
>> fitting method ( doi: 10.1002/jcc.23208) taking AM1 charge as an initial
>> guess.
>> Or you can hack the resp code by replacing LU decomposition with SVD
>> analysis and setting the null space to zero.
>>
>> Good luck,
>>
>> Ye
>>
>> On 10/27/2015 04:38 PM, Jérémie Knoops wrote:
>> > Dear Amber users,
>> >
>> > I'm trying to determine the charges for phenylguanidinium.
>> > I normally use the RED servers (and very often multiconfigurational fit)
>> > but the q4md website is still down.
>> > Using RESP and Gaussian with one conformation (minimized structure), I
>> get
>> > too high absolute values for them (up to 1.1 for a carbon atom,
>> > see GdPhenyl_resp.mol2).
>> > It's impossible to parametrize the molecule with those charges, the
>> > equilibrium bond length is 0.06 Å shorter than the reference bond
>> length.
>> >
>> > I tried the am1-bcc scheme, also with one conformation and the charges
>> > seem reliable (see GdPhenyl_am1-bcc.mol2). I can parametrize the torsion
>> > with them.
>> > Do I have to use the am1-bcc charges? Are they really reliable? Are
>> there
>> > other options?
>> >
>> > Thank you for your advice.
>> >
>> > *Jérémie Knoops*
>> >
>> > *PhD StudentLaboratory for Chemistry of Novel Materials
>> > <http://morris.umh.ac.be/default.aspx>*
>> > *University of Mons* <http://portail.umons.ac.be/en2/>
>> >
>> >
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Received on Mon Nov 02 2015 - 05:30:05 PST
