Thank you very much for this, Bruce. It will help me, for sure.
Could you just let me know where you found the parameters or how you
generated them?
Thanks in advance.
Regards,
Antoine
Le 5/02/2010 22:39, Bruce D. Ray a écrit :
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte
<antoinedelmo...@hotmail.com>
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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