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