[gmx-users] again about the non-standard residue and thank Dr. Mu

HR Hu hrhu75 at gmail.com
Fri Nov 4 09:30:59 CET 2005

Hi, Dr Mu,
 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?
  H. R. Hu

State Key laboratory of Genetic Engineering,

Scool of Life Sciences,

Fudan University

Handan road 220, Shanghai, 200433


 Message: 1
> Date: Thu, 3 Nov 2005 10:42:49 +0800
> From: "Mu Yuguang (Dr)" <YGMu at ntu.edu.sg>
> Subject: RE: [gmx-users] problems to constructe topology for
> non-standardresidues
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <48BABA4E8A54DF4AAF9CCF36D614027301967DA2 at EXCHANGE23.staff.main.ntu.edu.sg
> >
> Content-Type: text/plain; charset="us-ascii"
> Just in bonds segtion write
> -C N
> C +N
> Here -C means the C from last residue and +N is the N from next residue

Dr. Yuguang Mu
> Division of Structural and Computational Biology
> School of Biological Sciences
> Nanyang Technological University
> 60 Nanyang Drive
> Singapore 637551
> Tel: 63162885
> Fax: 67913856
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