AMBER Archive (2008)

Subject: Re: AMBER: concerning force fields

From: Karl Kirschner (kkirschn) (kkirschn_at_hamilton.edu)
Date: Fri Jun 27 2008 - 08:02:03 CDT

Hi Adrien,

    I have a couple of suggestions for you. There are two force fields that are included in the AMBER program package, GAFF and GLYCAM, that you might investigate using for n-alkanes. GAFF was developed for use with nonstandard residues, where nonstandard for AMBER typically means that they are not amino or nucleic acids. GLYCAM is a carbohydrate force field, but it should include all the force field terms necessary for simulating n-alkanes. These two force fields were developed using a slightly different philosophy, such as how assigns SCEE and SCNB during the simulation or how one determines the partial atomic charges for the molecule of interest. You should read both papers that outline their development, and understand their differences before using them. I would investigate these force fields before you try to develop a new one.

    I don't mean to be discouraging, but developing a new force field when you are also new to AMBER will be very difficult. It can take years to develop and fine tune a force field to model the physics of what you are interested in. To be able to do this with AMBER you need to know 1) how and what type of charges you wish to use, 2) how do you want to handle SCEE and SCNB, 3) what molecules will you use for your training and test set, 4) what specific geometric parameters will you need to parameterize, 5) what level of quantum theory do you wish to use to train and validate your parameter set, in addition to available experimental data, and 6) how to set up a constrained minimization using Sander. This is just to name a few issues.

    I also recommend reading some books/chapters concerning parameterization, such as Burkert and Allinger's Molecular Mechanics; Cramer's Essential of Computational Chemistry.

Cheers,
Karl
____________________________________
Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Visiting Assistant Professor
Hamilton College, Clinton NY 13323
____________________________________
----- Original Message -----
From: Adrien Delmont <adriendelmont_at_yahoo.com>
Date: Friday, June 27, 2008 2:25 pm
Subject: Re: AMBER: concerning force fields
To: amber_at_scripps.edu

> Dear  Simmerling,
> In fact, I just done some of the tutorials . And  I’m still
> working on them and also looking over them.  But I need to know
> some extra information about this issue  and need some expert
> advice and suggestions.  You mentioned about an important point
> that ‘How you proceed can depend on what type of molecules you
> want to simulate ‘  . So  according to my study what must I do
> to create different force fields.   In this sense, I’m waiting
> for your contributions.
> Many thanks in advance.
>
> Best regards,
>
> Adrien
>
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Thursday, June 26, 2008 10:25:04 PM
> Subject: Re: AMBER: concerning force fields
>
> Hi Adrien,
> have you worked through the tutorials on the web site?
> They can be helpful- if not, let us know that you're looking for
> more detail or so on.
> carlos
>
> 2008/6/26 Adrien Delmont <adriendelmont_at_yahoo.com>:
> > Dear  Simmerling,
> >
> > I want to say sorry because I completely forgot to mention my
> structure I
> > study on. I'm interested in  n-alkanes and  evaluating
> thermophysical and
> > structural properties of n- alkanes  and  binary mixtures  of
> n-alkanes.
> >  What are the main steps  and levels  of  creating a different
> force field?
> >  What must I do step by step ? In these conditions I 'm
> waiting for your
> > help and also all Amber user's help.
> >
> > Many thanks in advance.
> >
> >  Best regards,
> >
> > Adrien
> >
> > ----- Original Message ----
> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > To: amber_at_scripps.edu
> > Sent: Thursday, June 26, 2008 7:16:48 PM
> > Subject: Re: AMBER: concerning force fields
> >
> > have you checked the tutorials? There is a nice one there on
> force field
> > development for non-standard residues. I think your question
> is a bit too
> > open to get much help by email- are you interested in small molecule
> > force fields, unusual amino acids, sugars, etc? How you
> proceed can
> > depend on what type of molecules you want to simulate.
> >
> >
> > On Thu, Jun 26, 2008 at 11:14 AM, Adrien Delmont
> > <adriendelmont_at_yahoo.com> wrote:
> >> Dear All,
> >>
> >> I'm using Amber 9 v.  My goal is to create different force
> fields that
> >> Amber
> >> does not provide for my  molecular  structure.  I want to ask
> you some
> >> questions about creating different force fields in Amber . 
> What are the
> >> main steps and levels  of  creating a different force field?
> What must I
> >> do
> >> step by step ? Could you give me some information about this
> ? Please help
> >> me to understand the basics of this procedure.
> >>
> >> Many thanks in advance.
> >>
> >>  Best regards,
> >>
> >> Adrien
> >>

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