[gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

On Fri, May 25, 2012 at 4:15 PM, Francesca <francesca.stanzione at unina.it>wrote:

> can you write the atoms 6002 6004 6006 6017 6021 and all informations in
> your
> topology file about these atoms??
>
> Francesca
>

Sure:

>From the begining:

Unknown cmap torsion between atoms 799 801 804 811 813


; residue 399 NON rtp NON  q +0.6
   799          C    399    NON      C    799       0.62     12.011   ;
qtot -81.13
; residue 400 POL rtp POL  q -0.5
   800          N    400    POL      N    800      -0.47     14.007   ;
qtot -81.6
; residue   1 SER rtp SER  q  0.0
   801        NH2      1    SER      N    801      -0.96     14.007   ;
qtot -82.56
   802          H      1    SER    HT1    802       0.34      1.008   ;
qtot -82.22
   803          H      1    SER    HT2    803       0.34      1.008   ;
qtot -81.88
   804        CT1      1    SER     CA    804       0.19     12.011   ;
qtot -81.69
   805         HB      1    SER     HA    805       0.09      1.008   ;
qtot -81.6
   806        CT2      1    SER     CB    806       0.05     12.011   ;
qtot -81.55
   807         HA      1    SER    HB1    807       0.09      1.008   ;
qtot -81.46
   808         HA      1    SER    HB2    808       0.09      1.008   ;
qtot -81.37
   809        OH1      1    SER     OG    809      -0.66     15.999   ;
qtot -82.03
   810          H      1    SER    HG1    810       0.43      1.008   ;
qtot -81.6
   811          C      1    SER      C    811       0.51     12.011   ;
qtot -81.09
   812          O      1    SER      O    812      -0.51     15.999   ;
qtot -81.6
; residue   2 GLY rtp GLY  q  0.0
   813        NH1      2    GLY      N    813      -0.47     14.007   ;
qtot -82.07
   814          H      2    GLY     HN    814       0.31      1.008   ;
qtot -81.76
   815        CT2      2    GLY     CA    815      -0.02     12.011   ;
qtot -81.78
   816         HB      2    GLY    HA1    816       0.09      1.008   ;
qtot -81.69
   817         HB      2    GLY    HA2    817       0.09      1.008   ;
qtot -81.6
   818          C      2    GLY      C    818       0.51     12.011   ;
qtot -81.09
   819          O      2    GLY      O    819      -0.51     15.999   ;
qtot -81.6

Where NON and POL are residues made on my own (residue = atom) which are in
the aminoacids.rtp. I also added them to the residuetypes.dat. They form a
planar surface (400 of them). Is it because there is no data of cmap on
those atoms?
Why do I do this? I want to use distance restrain of my protein terminal
with one of the atoms belonging to the "surface" made of those created
atoms to mimic the attached protein to the surface. Maybe its easier to
form a bond?

Steven




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