[gmx-users] OPLS-AA force field

Jochen Hub jochen at xray.bmc.uu.se
Fri Oct 8 17:05:25 CEST 2010


see here for a start:




On 10/8/10 Oct 8,3:51 PM, lammps lammps wrote:
> Hi everybody,
> I want to use OPLS-AA force field to do simulation for dendrimer(see
> the attached files for figure and .pdb). If the pH<4.0,the tertiary
> amines on the dendrimer will be protonated, i.e. (CH2)3-N will be
> changed to (CH2)3-NH+. Now, I have two questions as follows.
> 1. How can I use pdb2gmx to get the .gro and .itp? It seems there are
> not the /residue./
> 2. I don't find the suitable force field for the N in (CH2)3-NH+, How
> can I deal with this?
> Any suggestion is appreciated. Thanks in advance.
> -- 
> wende

Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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