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<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>Dear Users,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>I am trying to
simulate a capped pentapeptide using OPLS force field. Pdb2gmx runs successfully
, however grompp gives following warnings<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>WARNING 1 [file
"topol.top", line 632]:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'> No default
Ryckaert-Bell. types, using zeroes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>WARNING 2 [file
"topol.top", line 857]:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'> No default
Ryckaert-Bell. types, using zeroes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>How should I proceed
if these parameters are missing in OPLS.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>The topology and
gro files are attached herewith<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>Regards,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face="MS Reference Sans Serif"><span
style='font-size:9.0pt;font-family:"MS Reference Sans Serif"'>Gurpreet<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face="MS Reference Sans Serif"><span style='font-size:10.0pt;font-family:
"MS Reference Sans Serif"'>-------------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><st1:place
w:st="on"><st1:PlaceType w:st="on"><font size=1 face="MS Reference Sans Serif"><span
style='font-size:7.5pt;font-family:"MS Reference Sans Serif"'>University</span></font></st1:PlaceType><font
size=1 face="MS Reference Sans Serif"><span style='font-size:7.5pt;font-family:
"MS Reference Sans Serif"'> of <st1:PlaceName w:st="on">Dortmund</st1:PlaceName></span></font></st1:place><br>
<font size=1 face="MS Reference Sans Serif"><span style='font-size:7.5pt;
font-family:"MS Reference Sans Serif"'>Department of Chemistry<br>
Physical Chemistry I - Biophysical Chemistry<br>
Otto-Hahn Str. 6<br>
D-44227 <st1:City w:st="on"><st1:place w:st="on">Dortmund</st1:place></st1:City><br>
<st1:country-region w:st="on"><st1:place w:st="on">Germany</st1:place></st1:country-region><br>
</span></font><font size=2 face="MS Reference Sans Serif"><span
style='font-size:10.0pt;font-family:"MS Reference Sans Serif"'><br>
</span></font><font size=1 face="MS Reference Sans Serif"><span
style='font-size:7.5pt;font-family:"MS Reference Sans Serif"'>Office:
C1-06 room 176<br>
Phone: +49 231 755 3916</span></font><font size=2><span style='font-size:
10.0pt'><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face="MS Reference Sans Serif"><span style='font-size:10.0pt;font-family:
"MS Reference Sans Serif"'>-------------------------------------------------</span></font><o:p></o:p></p>
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12.0pt'><o:p> </o:p></span></font></p>
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