Hi, see here for a start:
http://www.gromacs.org/Documentation/How-tos/Parameterization Cheers, Jochen 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 http://xray.bmc.uu.se/~jochen/index.html ---------------------------------------------------
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