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<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Dear Gromacs users,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>I obtained the ITP file
of glycerol molecule from the Dundee PRODRG server (<a
href="http://davapc1.bioch.dundee.ac.uk/programs/prodrg/">http://davapc1.bioch.dundee.ac.uk/programs/prodrg/</a>).
However, I heard that the charges are not accurate enough. So I estimated the
charges of glycerol using Gaussian. The input file of Gaussian is gol.gjf,
including all atoms of a glycerol molecule. The output of Gaussian is selected
as follows:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>--------------------------
Gaussian Output
---------------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Mulliken atomic charges:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
1 O -0.677102<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
2 H 0.422534<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
<st1:chmetcnv TCSC="0" NumberType="1" Negative="False" HasSpace="True"
SourceValue="3" UnitName="C" w:st="on">3 C</st1:chmetcnv>
-0.156687<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
4 H 0.224462<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
5 H 0.169912<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
<st1:chmetcnv TCSC="0" NumberType="1" Negative="False" HasSpace="True"
SourceValue="6" UnitName="C" w:st="on">6 C</st1:chmetcnv>
0.007200<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
7 H 0.182644<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
8 O -0.586768<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
9 H 0.435753<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'> <st1:chmetcnv
TCSC="0" NumberType="1" Negative="False" HasSpace="True" SourceValue="10"
UnitName="C" w:st="on">10 C</st1:chmetcnv> -0.171961<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'> </span></font><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt;
font-family:"Times New Roman"'>11 H 0.173527<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
12 H 0.190745<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
13 O -0.630544<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
14 H 0.416285<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'> Sum of Mulliken
charges= 0.00000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>-------------------------------------------END
of Gaussian Output ----------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>------------------------------------------
ITP file
----------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>[ atoms ]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>;
nr type resnr resid atom
cgnr charge mass<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
</span></font><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>1
OA 1 GOL
OAB 1 -0.095 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
2 HO 1
GOL HAA 1
0.043 1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
3 CH2 1
GOL CAA 1
0.052 14.0270 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
4 CH1 1
GOL CAC 2
0.078 13.0190 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=IT
style='font-size:12.0pt;font-family:"Times New Roman"'>
</span></font><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>5
OA 1 GOL
OAD 2 -0.114 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
6 HO 1
GOL HAB 2
0.036 1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
7 CH2 1
GOL CAE 3
0.053 14.0270 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
8 OA 1
GOL OAF 3
-0.095 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>
9 HO 1
GOL HAC 3
0.042 1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>-------------------------------------END
of ITP file
------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Then it comes to edit
the ITP file. But there are some problems puzzling me.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Firstly, the ITP file
just has 9 atoms ( see above) as the Dundee PRODRG server uses united-atom
force field which neglects 5 unpolar hydrogen atoms while the result of
Gaussian has 14 atoms. How should I edit the charges of ITP file? Or how could
I edit the cgnr and charge fields of the ITP file with the Gaussian result? Is
it reasonable and acceptable that a charge group has a decimal number of
charges?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Secondly, the charge
group number of ITP file is 3 whereas the result of Gaussian has only one
charge group(14 atoms as a whole group). Could the Gaussian package calculate
the charges of a molecules by first dividing the atoms of the molecule into
different charge groups? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Any help/suggestions
will be greatly appreciated!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Thank you!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-family:"Times New Roman"'>Chuan Liao<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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