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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I see what’s your meaning.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dr. Yuguang Mu</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Division of Structural and Computational
Biology</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
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color:navy'>School</span></font></st1:PlaceType><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'> of <st1:PlaceName
w:st="on">Biological</st1:PlaceName></span></font></st1:place><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> Sciences</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Nanyang Technological University</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:Street w:st="on"><st1:address w:st="on"><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>60 Nanyang Drive</span></font></st1:address></st1:Street><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
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size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> 637551</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Tel: 63162885</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Fax: 67913856</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'> </span></font><o:p></o:p></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>HR Hu<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, November 04, 2005
4:31 PM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] again about
the non-standard residue and thank Dr. Mu</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi, Dr Mu,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> 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? <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> H. R. Hu<br>
<br>
State Key laboratory of Genetic Engineering,<br>
<br>
Scool of Life Sciences,<br>
<br>
<st1:place w:st="on"><st1:PlaceName w:st="on">Fudan</st1:PlaceName> <st1:PlaceType
w:st="on">University</st1:PlaceType></st1:place><br>
<br>
<st1:City w:st="on">Handan</st1:City> road 220, <st1:City w:st="on"><st1:place
w:st="on">Shanghai</st1:place></st1:City>, 200433<br>
<br>
<st1:country-region w:st="on"><st1:place w:st="on">China</st1:place></st1:country-region><br>
<br>
<br>
<o:p></o:p></span></font></p>
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<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;
margin-left:4.8pt;margin-right:0in'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Message: 1<br>
Date: Thu, 3 Nov 2005 10:42:49 +0800<br>
From: "<st1:PersonName w:st="on">Mu Yuguang</st1:PersonName> (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: "<st1:PersonName w:st="on">Discussion list for GROMACS users</st1:PersonName>"
<<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<o:p></o:p></span></font></p>
</blockquote>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;
margin-left:4.8pt;margin-right:0in'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Dr. Yuguang Mu<br>
<br>
Division of Structural and Computational Biology<br>
<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">School</st1:PlaceType> of <st1:PlaceName
w:st="on">Biological</st1:PlaceName></st1:place> Sciences <br>
<br>
Nanyang Technological University<br>
<br>
<st1:Street w:st="on"><st1:address w:st="on">60 Nanyang Drive</st1:address></st1:Street><br>
<br>
<st1:country-region w:st="on"><st1:place w:st="on">Singapore</st1:place></st1:country-region>
637551<br>
<br>
Tel: 63162885<br>
<br>
Fax: 67913856<o:p></o:p></span></font></p>
</blockquote>
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