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.public.wh.hb.cn
==================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Sep 19 2003 - 14:53:00 PDT
