[gmx-users] Dear all Re: Topology file for phosphothreonine (TPO) for OPLS force field

[Justin A. Lemkul]

sumanth kumar wrote:
> Dear Bruce D.Ray...
> 
> I had used the TPO parameters as u gave in previous posts.
> 
> 
> [ *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
> 
> 
> And i added Ryckaert-Belleman dihedrals in ffoplsaabon.itp file basing 
> on the errors  got after i run pdb2gmx command.
> 
> And i had left the 6 coefficients (c0 to c5) as 0.0000 because i dunno 
> how to derive those values.
> 
> So please help me how to fill those values. I had gone through the RB 
> dihedrals main article but im not clear.
> 

The fitting procedures are described in great detail in both of the OPLS papers 
(Jorgensen JACS 1996 and Kaminski J Phys Chem B 2001).  If there is a specific 
point or technique that you're not familiar with, you'll have better luck asking 
a very specific question rather than "I don't know how to do it, someone tell me 
how."

-Justin

> Just give me sugggestions to derive those values and if u have those 
> values it would me much more easier for me....:-)
> 
> Thank you in advance
> sumanth
> 
> 
> -- 
> *SUMANTH KUMAR.M*
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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