[gmx-users] How to include bonded parameters in ffgmxbon.itp?

[Alexandre Suman de Araujo]

Hi GMXer

I'm trying to include parameters to acetonitrile in ffgmxnb.itp and
ffgmxbon.itp. The Non-bonded parameters I can include using LJ parameters
and charges found in some papers. My doubt is how to find(or calculate)
bonded parameters to include in ffgmxbon.itp?

Thank's and waiting answers

[]'s
Alexandre Suman de Araujo
IFSC - USP - São Carlos
UIN: 6194055
----- Original Message -----
From: "K.A. Feenstra" <Feenstra at chem.vu.nl>
To: <gmx-users at gromacs.org>
Sent: Monday, August 19, 2002 5:25 AM
Subject: Re: [gmx-users] genbox problems


> David wrote:
> >
> > On Sun, 2002-08-18 at 14:33, Chris Shaw wrote:
> > >
> > > Hi all,
> > >
> > > Just a quick question. I am getting a feel of gromacs by playing
around with helices in different solvents. My problem is that genbox
re-writes the .gro file to represent the addition of solvent molecules, but
doesn't re-write the .top file to reflect the changes. When I attempt to add
the .itp file for example dmso.itp into the top file with the #include
command it doesn't seem to register and i get an error back re not being
able to define SD atom types. Could any one help, as I am sure that i am
doing something fundamentally wrong.
> > >
> > Probably SD is not in the force field you are using for the protein. In
> > GROMOS96 the atom types may be named differently. Just check all the
> > topology files, including those from the library (gromacs/share/top).
> > With the manual in hand it should be straightforward to sort out.
>
> In the Gromos97 ff's (ffG43*) the DMSO atom types are called SDMSO,
> CDMSO and ODMSO (as per ffG43a2.atp). We should have edited the dmso.itp
> file to be forcefield sensitive, as spc.itp is.
>
> --
> Groetjes,
>
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
> |________|___________________________________________________________|
>
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