Hi Chirag Vora,
Thank you so much for the letter. It seems to me that I have to use
antechamber for doing this. I thought there might be some ordinary charge
values available without calculating them. Do you have any idea of my second
question? Thanks a lot!
Lan
On Fri, Sep 2, 2011 at 3:13 PM, Chirag Vora <chirag740.gmail.com> wrote:
> In our lab we use GAFF for a polymer system (dendrimer).
>
> About obtaining charges.
> Yes, using antechamber it is possible to derive RESP charges for polymer.
> See this link: ambermd.org/antechamber/ac.html
>
>
> Chirag Vora
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Sector 67, S.A.S. Nagar (Mohali) - 160062
> Punjab, INDIA
>
> Sent from my BlackBerry® smartphone from !DEA
>
> -----Original Message-----
> From: su He <susu5233.gmail.com>
> Date: Fri, 2 Sep 2011 14:58:06
> To: <amber.ambermd.org>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] some questions on GAFF
>
> Dear Amber uses,
>
> I'm trying to use GAFF to describe the interaction in a polymer system. I
> have parameter data files of GAFF and already read them several times. Now
> I
> have some questions on this force field.
>
> The first one is about atomic charges. I couldn't find the charge value for
> any given atom. It seems to me that the charge value is obtained by running
> some tool in Amber software package. Is it right? Does anyone know other
> ways to obtain atomic charges for a simple polymer (let's say, the repeat
> units in a polymer chain only include three types of atoms: C3,C2 and hc,
> only have five types of bonds: C3-C3,C2-C2,C3-C2,HC-C3,HC-C2) without using
> any Amber tools?
>
> The second one is about the total number of dihedrals. Is it necessary to
> use the torsion potential of GAFF for all the dihedrals? For instance, for
> a
> chemical structure like CH3-CH=CH-CH3, do I need to take care of all the
> dihedrals (the total number: 12): C3-C2-C2-C3, Hc(1)-C3-C2-C2,
> Hc(2)-C3-C2-C2, Hc(3)-C3-C2-C2, Hc(1)-C3-C2-Hc,Hc(2)-C3-C2-Hc,
> Hc(3)-C3-C2-Hc,Hc-C2=C2-C3,Hc-C2=C2-Hc,Hc-C2-C3-Hc(1), Hc-C2-C3-Hc(2),
> Hc-C2-C3-Hc(3)? If so, I could find the parameter values for X-C3-C3-X,
> X-C2-C2-X, X-C3-C2-X, HC-C3-C2-C2, but I could not find the parameter
> values
> for Hc-C3-C3-Hc, Hc-C2-C2-HC, Hc-C2-C2-C3, Hc-C3-C2-Hc? Then, do it means,
> I
> have to use the same values in the generalized forms: X-C3-C3-X, X-C2-C2-X,
> X-C3-C2-X for the dihedrals with carbon-hydrogen bonds?
>
> Does anyone use the GAFF for some polymer systems? Your any suggestions or
> experience will be highly appreciated.
>
> Lan
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Received on Fri Sep 02 2011 - 13:30:03 PDT
