AMBER Archive (2004)

Subject: AMBER: Questions on simulating dendrimer in AMBER.

From: Hwankyu Lee (leehk_at_umich.edu)
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.

best,
Hwankyu.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu