<br><br><div class="gmail_quote">On Fri, May 25, 2012 at 4:15 PM, Francesca <span dir="ltr"><<a href="mailto:francesca.stanzione@unina.it" target="_blank">francesca.stanzione@unina.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
can you write the atoms 6002 6004 6006 6017 6021 and all informations in your<br>
topology file about these atoms??<br>
<br>
Francesca<br></blockquote><div><br>Sure:<br><br>From the begining:<br><br>Unknown cmap torsion between atoms 799 801 804 811 813<br><br><br>; residue 399 NON rtp NON q +0.6<br> 799 C 399 NON C 799 0.62 12.011 ; qtot -81.13<br>
; residue 400 POL rtp POL q -0.5<br> 800 N 400 POL N 800 -0.47 14.007 ; qtot -81.6<br>; residue 1 SER rtp SER q 0.0<br> 801 NH2 1 SER N 801 -0.96 14.007 ; qtot -82.56<br>
802 H 1 SER HT1 802 0.34 1.008 ; qtot -82.22<br> 803 H 1 SER HT2 803 0.34 1.008 ; qtot -81.88<br> 804 CT1 1 SER CA 804 0.19 12.011 ; qtot -81.69<br>
805 HB 1 SER HA 805 0.09 1.008 ; qtot -81.6<br> 806 CT2 1 SER CB 806 0.05 12.011 ; qtot -81.55<br> 807 HA 1 SER HB1 807 0.09 1.008 ; qtot -81.46<br>
808 HA 1 SER HB2 808 0.09 1.008 ; qtot -81.37<br> 809 OH1 1 SER OG 809 -0.66 15.999 ; qtot -82.03<br> 810 H 1 SER HG1 810 0.43 1.008 ; qtot -81.6<br>
811 C 1 SER C 811 0.51 12.011 ; qtot -81.09<br> 812 O 1 SER O 812 -0.51 15.999 ; qtot -81.6<br>; residue 2 GLY rtp GLY q 0.0<br> 813 NH1 2 GLY N 813 -0.47 14.007 ; qtot -82.07<br>
814 H 2 GLY HN 814 0.31 1.008 ; qtot -81.76<br> 815 CT2 2 GLY CA 815 -0.02 12.011 ; qtot -81.78<br> 816 HB 2 GLY HA1 816 0.09 1.008 ; qtot -81.69<br>
817 HB 2 GLY HA2 817 0.09 1.008 ; qtot -81.6<br> 818 C 2 GLY C 818 0.51 12.011 ; qtot -81.09<br> 819 O 2 GLY O 819 -0.51 15.999 ; qtot -81.6<br>
<br>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?<br>
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? <br>
<br>Steven<br><br><br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
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