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

[Mu Yuguang (Dr)]

I see what's your meaning.

Yes, normally you should add some terminal parts CO CH3 , or NH-Ch3 to
saturate the group then using QM to get the partial charges.

 

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

 

________________________________

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of HR Hu
Sent: Friday, November 04, 2005 4:31 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] again about the non-standard residue and thank Dr.
Mu

 

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

China


 

	Message: 1
	Date: Thu, 3 Nov 2005 10:42:49 +0800
	From: "Mu Yuguang (Dr)" < YGMu at ntu.edu.sg
<mailto: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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