AMBER Archive (2003)

Subject: AMBER: no defined type for atom N atom

From: Wu Yingliang (wuyliang_at_public.wh.hb.cn)
Date: Fri Sep 19 2003 - 08:02:31 CDT

Dear Amber users,

Very Sorry for left out information by just sent email, I am using amber7 in Linux and ff99 force field!

I have a short peptide (about 30 residues) aminated in the C terminal. When I load it in xleap program, it tells me: there is no defined type for heavy atom N. In order to produce corresponding topology and coordinate file, I have to delete it, and atom OXT was then added.

Because this NH2 from aminated residues in the C terminal is important to interact with Receptor, another protein. Then how will I resolve such question for retaining NH2 during using SAVEAMBERPARM? Then I can use MD for my docked protein complex.

I am not a experienced user, and expect your help! Thanks a lot in advance!

Best Regards,

Wu Yingliang
2003-09-19
==================================
College of Life Sciences
Wuhan University
Wuhan 430072
China
Email: wuyliang_at_public.wh.hb.cn
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