<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><span style="font-family: tahoma,new york,times,serif;">On </span><font style="font-family: tahoma,new york,times,serif;" face="Tahoma" size="2">Fri, February 5, 2010 at 1:06:34 PM, </font><font face="Tahoma" size="2"><span style="font-family: tahoma,new york,times,serif;">Antoine Delmotte <antoinedelmotte@hotmail.com><br>wrote:</span><br></font><div>> I would like to simulate the CDK9 protein (3BLH in PDB), but there is
one residue (TPO,<br>> phosphothreonine), which Gromacs does not recognise.<br>> <br>> I
found the PRODRG website as well as force field parameters for TPO for
the Gromos96.1<br>> force field. However, I would like to use the OPLS-AA
force field. I therefore need a topology<br>> file for this force field,
which cannot be provided by PRODRG (only useful for united atoms<br>> force
fields).<br>> <br>> Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS<br>> force field?<br>> <br>> Otherwise, could someone give me clues or the link to a good tutorial about how to create<br>> this itp file myself? <br>> <br>> Molecular
dynamics is something completely new for me so, sorry if I ask stupid
questions.<br>> It also seems I am not the first one to have this problem
but I could not find any solution on<br>> the archive of the mailing list.<br><br>The charges probably need a little more work, but this might be a start towards an<br>rtp file for phosphothreonine to add to ffoplsaa.rtp.<br><br><font size="1"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">[ TPO ]</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> [ atoms ]</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> N opls_238 -0.500 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> H
opls_241 0.300 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CA opls_224B 0.140 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HA opls_140 0.060 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CB opls_158 0.205 2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"> HB opls_140 0.060 2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> OG1 opls_447 -0.700 2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> P opls_445 1.795 3</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O1P opls_446 -1.120 3</span><br style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O2P opls_446 -1.120 3</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O3P opls_446 -1.120 3</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CG2 opls_135 -0.180 4</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HG21 opls_140 0.060 4</span><br
style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HG22 opls_140 0.060 4</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HG23 opls_140 0.060 4</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> C opls_235 0.500 5</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O opls_236
-0.500 5</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> [ bonds ]</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> N H</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> N CA</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CA HA</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"> CA CB</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CA C</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CB HB</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CB OG1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CB CG2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span
style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> OG1 P</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O1P P</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O2P P</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> O3P P</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CG2 HG21</span><br style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CG2 HG22</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CG2 HG23</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> C O</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> -C N</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> [ dihedrals ] ; override some of the typebased
dihedrals</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> N CA CB OG1 dih_SER_THR_chi1_N_C_C_O</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family:
Courier New,courier,monaco,monospace,sans-serif;"> [ impropers ]</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> -C CA N H improper_Z_N_X_Y </span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> CA +N C O improper_O_C_X_Y </span></font><br><br><br>I hope that helps.<br><br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div>
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