AMBER Archive (2004)

Subject: AMBER: Questions on simulating dendrimer in AMBER.

From: Hwankyu Lee (
Date: Sun Sep 19 2004 - 22:21:03 CDT

Dear Amber-users,

I'm trying to simulate dendrimer, which is huge macromolecule and has
repeated structures, in AMBER. Could you answer some questions ?

1) How can I make a coordinate file (pdb) of dendrimer for AMBER? Can
I use a specific tool to build coordinates of dendrimer?? If so, the
tool is compatible with AMBER package?

2) After making pdb file, how can I create topology file for the
dendrimer? I'm wondering how I get the parameters (partial charges,
e.g.) for the topology for the dendrimer.

Thanks for your help in advance.


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