AMBER Archive (2004)

Subject: AMBER: how to use prep file

From: Fang, Jianwen (jwfang_at_ku.edu)
Date: Mon Feb 23 2004 - 13:15:19 CST

        Dear all,
        I have a naive question. How should I use prep and frcmod files which I download from amber parameter database, to generate prmtop and prmcrd files for a cofactor I have pdb file. Do I need to modify atom types in my pdb file? Also how to construct a larger system which has this cofactor?
        Thanks!
        JF
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