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Thank you very much for this, Bruce. It will help me, for sure. <br>
<br>
Could you just let me know where you found the parameters or how you
generated them?<br>
<br>
Thanks in advance.<br>
<br>
Regards,<br>
<br>
Antoine<br>
<br>
Le 5/02/2010 22:39, Bruce D. Ray a écrit :
<blockquote cite="mid:452521.65015.qm@web35801.mail.mud.yahoo.com"
type="cite">
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<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
<a class="moz-txt-link-rfc2396E" href="mailto:antoinedelmotte@hotmail.com"><antoinedelmotte@hotmail.com></a><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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