RE : [gmx-users] Does Gromacs work on a molecule which is not protein

[Diane Fournier]

For molecules which are not amino acids, DNA or RNA, you have to write a topology yourself. There are some tools that can help you with that. If you plan to use the gromacs united-atom forcefield (ffgmx), you can try PRODRG, which is available on the Dundee server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/). It will give you a .itp file (information on the molecule itself) to which you will have to add some system information (some includes, like forcefiled type, water .itp file, etc). The format of the .top file is given in the user's manual. But be careful to edit the file PRODRG gives you, because sometimes there are errors in the atom types assignation and in the partial charges that are given (you can compare with charges calculated with a quantum mechanical software, like Gaussian or MOPAC). 
 
If you plan to use another forcefield, you will have to write the topology yourself (atom types & charges, bond parameters, angle parameters, dihedrals and improper), using the descriptions of the atom types given in the forcefield's .atp file. Check also in the contributed software section for some programs that can convert one format of topology (ex.: AMBER or TINKER) to gromacs format. The .pdb file can be transformed into a .gro using the editconf program.
 
Hope that helps
 
Diane
   

________________________________

De: gmx-users-bounces at gromacs.org de la part de Tanping Li
Date: mer. 2006-05-17 10:58
À: Discussion list for GROMACS users
Objet : [gmx-users] Does Gromacs work on a molecule which is not protein



Dear all,

I plan to run solvate a small molecule using Gromacs.
This small molecule is not a protein or DNA or RNA. So
I meet the problem at the first step to run pdb2gmx,
the wrong information says Gromacs can't recognize
this molecule.
Is there a way to assign charge to this small molecule
and get a *.top file; could I use gromacs to run this
unknown small molecule?

Thank you very much for your suggestion. I have
bothered by this for a while.


Best
Tanping
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