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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'>This charm 27 force field was used with gromacs
3.1 and 3.2 . I did not use it with gromacs 3.3.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I think maybe there are some differences
between 3.1, 3.2 and 3.3 in creating terminal groups.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Anyway as I suggested in the readme file
that you can prepare the pdb file with original charm program including add
hydrogen atoms, terminals, et.al. Then just use pdb2gmx to create top file with
–ter switch answered by none.</span></font></p>
<div>
<p><font size=2 color=navy face="Times New Roman"><span style='font-size:10.0pt;
color:navy'>Regards<br>
Yuguang<br>
<br>
Dr. Yuguang Mu<br>
Division of Computational and Structrual Biology<br>
</span></font><font size=2 color=navy><span style='font-size:10.0pt;color:navy'>School</span></font><font
size=2 color=navy><span style='font-size:10.0pt;color:navy'> of </span></font><font
size=2 color=navy><span style='font-size:10.0pt;color:navy'>Biological</span></font><font
size=2 color=navy><span style='font-size:10.0pt;color:navy'> Sciences<br>
Nanyang Technological University<br>
</span></font><font size=2 color=navy><span style='font-size:10.0pt;color:navy'>Singapore</span></font><font
size=2 color=navy><span style='font-size:10.0pt;color:navy'> 637820<br>
Tel: 0065-63162885<br>
Mail: ygmu@ntu.edu.sg</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>leafyoung81-group@yahoo.com<br>
<b><span style='font-weight:bold'>Sent:</span></b> 2005</span></font><font
size=2 face=宋体><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>年</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>12</span></font><font
size=2 face=宋体><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>月</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>24</span></font><font
size=2 face=宋体><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>日</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> </span></font><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>14:28</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>To:</span></b> Discussion list for GROMACS
users<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] using
charmm force fields with gmx v3.3</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>This CHARM27 FF is supposed to be used by Gromacs 3.3.
You may check ffgmx2-c.tdb from different versions of gromacs and change the
file format accordingly.<br>
<br>
Yang Ye<br>
<br>
----- Original Message ----<br>
From: dimka <newyorkdimka@gmail.com><br>
To: gmx-users@gromacs.org<br>
Sent: Saturday, December 24, 2005 7:37:23 AM<br>
Subject: [gmx-users] using charmm force fields with gmx v3.3<br>
<br>
Hello, I've downloaded charmm27 force fields (from <a
href="http://www.gromacs.org/topologies/force_fields.php" target="_blank"
id=bodyLinks>http://www.gromacs.org/topologies/force_fields.php</a>) and
followed installation instructions.<br>
When I try to generate topology and structure file I'm getting the following
using Charmm27 ff I'm g etting the following error:<br>
<br>
</span></font><font face="Courier New"><span style='font-family:"Courier New"'><br>
Opening library file /usr/gmx/share/gromacs/top/ffcharmm-n.tdb<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3<br>
Source code file: ter_db.c, line: 85<br>
<br>
Fatal error:<br>
Reading Termini Database: expected 3 items of atom data in stead of 1 on line<br>
N &nbs
p; NH3 14.0027 -0.3000<br>
-------------------------------------------------------<br>
</span></font><br>
I spent some time trying looking at the ffcharmm-n.tdb but i cannot figure out
its format.<br>
Can anyone point me to the description of the file format?<br>
<br>
Dmitry</p>
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