[gmx-users] Using GROMACS with small molecules

[Daan van Aalten]

Hi Alexandre

GROMACS itself does not have the capability of generating topologies for
non-protein/dna small molecules. However, you can automatically generate
topologies for almost any small molecule made up of H,C,N,O,P,S,F,Cl,Br,I
with PRODRG, see
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html

You mention you want to include metals, which PRODRG currently
does not support. You could however, fake things by replacing your metals
with P,C or S and then altering values for non-bonded parameters later by
hand.

Hope this helps

cheers

Daan

 
On Sun, 9 Dec 2001, Alexandre Suman de Araujo wrote:

> Hi guys
> 
> It's my first message to the list and I'm a begginer in molecular dynamics. A friend of mine that work with molecular dynamics of proteins told me about GROMACS and that I could use it to make my simulations of small organometalics molecules.
> I installed GROMACS in my PC and I read a good part of manual and the archieve of this list and I still have the following doubt: Can I use GROMACS to make my simulations of small organometalics molecules with relative easiness and with good results???
> If somebody work with this type of simulation, every help is welcome. If GROMACS is not a good choice to make this simulations, can somebody advise me which one(or ones) are good???
> Thank's a lot.
> 
> Alexandre Suman de Araujo
> IFSC - USP - São Carlos
> UIN: 6194055
> 


##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
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