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

sumanth kumar sumanthkumar07 at gmail.com
Tue Jul 27 13:58:58 CEST 2010

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.

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100727/daa27675/attachment.html>

More information about the gromacs.org_gmx-users mailing list