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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 gmx 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"'><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
manually make a topology file for a peptide with few substitutions. I had
trouble in understanding regarding assignment of dihedral paramaters in opls by
grompp. As far as I understood, ffoplsaabond.itp contains all the dihedral
parameters where the bond_type from ffoplsaanb.itp are used to define the dihedral
angles. <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"'>If I take an
entry from ffoplsaa.rtb for example glycine,<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"'>[ GLY ]<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"'> [ atoms ]<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"'>
N opls_238 -0.500 1<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"'>
H opls_241 0.300 1<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"'>
CA opls_223B 0.080 1<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"'>
HA1 opls_140 0.060
1<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"'>
HA2 opls_140 0.060
1<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"'>
C opls_235 0.500 2<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 opls_236 -0.500 2<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"'><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"'>And search for a
dihedral H-CA-C-O in ffoplsbon.itp, I don’t find any entries. Probably, I
have to look for the bond_type corresponding to opls_??? entries and then
search in ffoplsaabond.itp. It means that the first column entries in rtb file
is only used to map PDB atom types to opls atom types and is of no further use.
Please let me know if I am wrong.<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"'>With 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 Singh <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><b><font size=1 face="MS Reference Sans Serif"><span
style='font-size:8.0pt;font-family:"MS Reference Sans Serif";font-weight:bold'>-------------------------------------------------<o:p></o:p></span></font></b></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><b><font
size=1 face="MS Reference Sans Serif"><span style='font-size:8.0pt;
font-family:"MS Reference Sans Serif";font-weight:bold'>University</span></font></b></st1:PlaceType><b><font
size=1 face="MS Reference Sans Serif"><span style='font-size:8.0pt;font-family:
"MS Reference Sans Serif";font-weight:bold'> of <st1:PlaceName w:st="on">Dortmund</st1:PlaceName></span></font></b></st1:place><br>
<b><font size=1 face="MS Reference Sans Serif"><span style='font-size:8.0pt;
font-family:"MS Reference Sans Serif";font-weight:bold'>Department of Chemistry<br>
Physical Chemistry I - Biophysical Chemistry<br>
Otto-Hahn Str. 6<br>
D-44227 <st1:City w:st="on">Dortmund</st1:City><br>
<st1:country-region w:st="on"><st1:place w:st="on">Germany</st1:place></st1:country-region><br>
Office: C1-06 room 176<br>
Phone: +49 231 755 3916<o:p></o:p></span></font></b></p>
<p class=MsoNormal><b><font size=1 face="MS Reference Sans Serif"><span
style='font-size:8.0pt;font-family:"MS Reference Sans Serif";font-weight:bold'>Fax:
+49 231 755 3901<o:p></o:p></span></font></b></p>
<p style='margin:0cm;margin-bottom:.0001pt'><b><font size=1
face="MS Reference Sans Serif"><span style='font-size:8.0pt;font-family:"MS Reference Sans Serif";
font-weight:bold'>-------------------------------------------------</span></font></b><b><font
size=1 face="MS Reference Sans Serif"><span style='font-size:8.0pt;font-family:
"MS Reference Sans Serif";font-weight:bold'><o:p></o:p></span></font></b></p>
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