[gmx-users] Re: Gromacs Help

Anton Feenstra feenstra at chem.vu.nl
Tue Sep 2 09:26:02 CEST 2003

Lee Cheng Siang wrote:
> My name is Kenichi and I'm a graduate student in France doing MD  
> simulations on polymer systems. I got your e-mails from the gmx-user  
> group while trying to figure out how to build topology files for my  
> polymer to get it submitted under Gromacs for MD simulation.
> I did not really understand the thread in gmx-user list discussion. So  
> may I have some more clarification on how did you manage to solve the  
> problem? Or, could you please re-direct me to available ressources for  
> my problem, please?

I just noticed your e-mail sitting in my inbox, apparently forgotten.
Apologies for the (long) delay. However, I must say I cannot say much
to help you. If pdb2gmx doesn't work, that means your monomers are not
part of the standard residue topology database (rtp), so you will have
to write your own topologies. x2top is (from what I hear, I never needed
it) a reasonable program, but for many molecules the ProDrg web-server
(look on the gmx-users list or gromacs web-site for the adress of ProDrg)
works great. Often you will need to manually adjust the topologies, e.g.
add charges, and you will have to convert the .top/.itp topology to an
'.rtp' type topology. For example, you have to provide 'rules' for the
connectivity between your monomers. This tends to be a lot of work.
The relevant chapters in the manual (e.g. 'Topology' and something about
file formats) should get you started. You can have a look at the existing
.rtp entries for e.g. amino-acid residues to get an idea of how it is done.

Please feel free to ask again (preferably on the list) if you get (or
remain) stuck.

Good luck!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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