<div>Hi, Dr Mu,</div>
<div> Thank you for your reply. Maybe I haven't said quite clear. To construct the topology file for the non-standard residue, we have to extract this strange aminoacid, then take it as a whole neutral molecule to minimize the structure and to calculate the charge population on every atom with MM or even QM method. whether should I add group such as -COCH3 and NH2 to the NH and CO terminal respectively to semi-reproduce the environment of these two terminal. How about your advice and experiences?
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<div> H. R. Hu<br><br>State Key laboratory of Genetic Engineering,<br><br>Scool of Life Sciences,<br><br>Fudan University<br><br>Handan road 220, Shanghai, 200433<br><br>China<br><br><br> </div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Message: 1<br>Date: Thu, 3 Nov 2005 10:42:49 +0800<br>From: "Mu Yuguang (Dr)" <<a href="mailto:YGMu@ntu.edu.sg">
YGMu@ntu.edu.sg</a>><br>Subject: RE: [gmx-users] problems to constructe topology for<br> non-standardresidues<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a>><br>Message-ID:<br> <<a href="mailto:48BABA4E8A54DF4AAF9CCF36D614027301967DA2@EXCHANGE23.staff.main.ntu.edu.sg">48BABA4E8A54DF4AAF9CCF36D614027301967DA2@EXCHANGE23.staff.main.ntu.edu.sg</a>><br><br>Content-Type: text/plain; charset="us-ascii"
<br><br>Just in bonds segtion write<br><br>-C N<br><br>C +N<br><br>Here -C means the C from last residue and +N is the N from next residue</blockquote>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dr. Yuguang Mu<br><br>Division of Structural and Computational Biology<br><br>School of Biological Sciences
<br><br>Nanyang Technological University<br><br>60 Nanyang Drive<br><br>Singapore 637551<br><br>Tel: 63162885<br><br>Fax: 67913856<br><br></blockquote></div>