[gmx-users] Could gromacs process RNA?

Luca Mollica mollica.luca at hsr.it
Thu Nov 20 12:38:01 CET 2003

 > Message: 8
 > From: "wang chuanming" <chuanmingwang at hotmail.com>
 > To: gmx-users at gromacs.org
 > Date: Thu, 20 Nov 2003 16:47:05 +0800
 > Subject: [gmx-users] Could gromacs process RNA?
 > Reply-To: gmx-users at gromacs.org
 > Dear all,
 > I have noticed that most works using gromacs were related to proteins 
 > or lipids. Are there anyone use it for research on RNA? There are 
very > few building block in the ff***.rtp or  .itp files, I think. Maybe
 > users must set up their block and it is difficult for me.

Dear Wang,

I'm not an expert using GROMACS for nucleic acids simulation, because 
I'm interested in proteins and lipids, like most of the users....but, a 
general rule that must be adopted in analysing a new problem in GROMACS, 
according to my opinion and experience, is that the user must build a 
new topology for every molecule except protein that he/she will have to 
use in the simulation. Also lipids are not by default included in 
GROMACS, but other users have built FF including parameters for lipids, 
and topologies .itp files as well.
This site could be very helpful, please try to use it, and you will 
discover some insights in creating topologies:


The Dundee PRODRG server is a free server that builds topologies for 
molecules provided by the user.
But also search for advices in the whole mailing list and topologies and 
force fields all over the web.

 > And MD of RNA usually needs
 > to add ion in the SOL, how can I do it?

It depends on HOW MANY ions do you need: e.g., if your system has a 
global charge of +3, you will have to replace 3 molecules of solvent 
with three Cl(-) ions. In this case, you will add in your topology file 
the line


and the final part of topology file

[ molecules ]
; Compound        #mols
Protein          1
SOL             1200

will become as follows:

[ molecules ]
; Compound        #mols
Protein          1
SOL             1197
CL               3

Good luck, and enjoy MD!


 > Expecting your reply
 > Thanks in advance!


Luca Mollica
Dulbecco Telethon Institute (Protein Structure Laboratory)

DIBIT-HSR,Via Olgettina 58
20132 Milano (Italy)

Tel: 0039-02-26434824
Fax: 0039-02-26434813
E-mail: mollica.luca at hsr.it

DTI website: http://www.telethon.it/dti/

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