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
<<attachment: g2.gif>>
Dendrim.pdb
Description: Protein Databank data
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