AMBER Archive (2009)

Subject: [AMBER] Re: pls help and suggest

From: Gustavo Seabra (
Date: Thu Jul 09 2009 - 11:14:42 CDT

Hi Vishal,

In the future, please send those questions directly to the Amber list.
There people with better experience in these areas can give you more
specific answers. I'm also forwarding this answer to the mailing list,
so if anyone there has better experience with those issues they can
give you a better answer.

On Thu, Jul 9, 2009 at 1:54 AM, Vishal Maingi wrote:
> Dear Sir,
> I am working on Dendrimer class of nanoparticles. I need your suggestions regarding force fields (ff)
> please suggest which ff can be used for dendrimer class. as GAFF ff is for small organic molecules
> and other ff are for NA , proteins and carbohydrates I cannot use them.

>From what I know, a dendrimer can be broken down in a few simpler
units. What you can do is to break your dendrimer in smaller units,
and parameterize those units individually, then use LEaP to build the
input files.

> pls suggest some ff which can be used alone or in combination

See above.

>  also parmchk and antechamber (limited to 200 atoms) cant be used to  find
> missing parameter in  and to define atom type and charge on Dendrimer.

You are right, those tools are not designed for such big molecules.
Again, the trick here is to find some simpler units to break your
dendrimer and parameterize those.

> I didnt get reply from archive. in archive I searched it was mentioned that we can use
> antechamber for small residues then we can join them later. but ultmately we have to define
> some ff for saving prmtop file.

Exactly. Once you find out the units, use GAFF for the parameters.

> any suggestion is highly appreciated
> pls pls reply
> thanks
> Vishal

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q:      Why do mountain climbers rope themselves together?
A:      To prevent the sensible ones from going home.

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