Thanks Justin, I used specbond.dat with a 0.15nm searching distance to create the bond, it seemed to work.
Ramon On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jose Tusell wrote: > >> Hi, >> >> I'm trying to construct diketopiperazine with gromacs. The problem that I >> have right now is forming the bond that unites the C and N termi to make the >> cyclic peptide. I tried using specbond.dat but so far I've been >> unsucessful. Here is my specbond.dat file and pdb file: >> >> > I believe there is a fundamental limitation with pdb2gmx - it doesn't deal > with cyclic species. Every post I've seen about this issue has been along > the lines of "generate the normal topology and add the missing bonded > parameters manually." > > I also think the specbond.dat file could never work anyway. The distance > between your C and N atoms appears to be right about 0.15 nm, so a 0.2-nm > criterion (+/- 10%) will never detect that a bond should be created between > these two atoms anyway. Just FYI for the future. > > -Justin > > > specbond.dat >> 8 >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 >> CYS SG 1 HEME FE 2 0.25 CYS2 HEME >> CYS SG 1 HEME CAB 1 0.18 CYS2 HEME >> CYS SG 1 HEME CAC 1 0.18 CYS2 HEME >> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME >> MET SD 1 HEME FE 1 0.24 MET HEME >> CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 >> TRP N 1 HISH C 1 0.2 TRP HISH >> >> whdikp.pdb >> REMARK S 14 x 14 mn oif >> ATOM 1 N TRP 1 -0.813 0.594 1.164 >> ATOM 2 H TRP 1 -0.249 1.064 1.843 >> ATOM 3 CA TRP 1 -0.264 -0.210 0.004 >> ATOM 4 HA TRP 1 0.855 -0.244 0.066 >> ATOM 5 CB TRP 1 -0.633 0.484 -1.321 >> ATOM 6 HB1 TRP 1 -1.672 0.344 -1.531 >> ATOM 7 HB2 TRP 1 -0.408 1.528 -1.262 >> ATOM 8 CG TRP 1 0.205 -0.166 -2.397 >> ATOM 9 CD1 TRP 1 0.227 -1.464 -2.727 >> ATOM 10 HD1 TRP 1 -0.407 -2.173 -2.195 >> ATOM 11 CD2 TRP 1 1.119 0.455 -3.258 >> ATOM 12 NE1 TRP 1 1.166 -1.607 -3.796 >> ATOM 13 HE1 TRP 1 1.401 -2.473 -4.259 >> ATOM 14 CE2 TRP 1 1.673 -0.432 -4.078 >> ATOM 15 CE3 TRP 1 1.485 1.803 -3.344 >> ATOM 16 HE3 TRP 1 1.065 2.575 -2.699 >> ATOM 17 CZ2 TRP 1 2.626 -0.117 -5.054 >> ATOM 18 HZ2 TRP 1 3.035 -0.902 -5.690 >> ATOM 19 CZ3 TRP 1 2.444 2.145 -4.320 >> ATOM 20 HZ3 TRP 1 2.741 3.190 -4.402 >> ATOM 21 CH2 TRP 1 2.990 1.222 -5.140 >> ATOM 22 HH2 TRP 1 3.727 1.540 -5.878 >> ATOM 23 C TRP 1 -0.816 -1.621 0.004 >> ATOM 24 O TRP 1 -0.072 -2.712 0.004 >> ATOM 25 N HISH 2 -2.331 -1.621 0.004 >> ATOM 26 H HISH 2 -2.895 -2.093 -0.674 >> ATOM 27 CA HISH 2 -2.881 -0.816 1.162 >> ATOM 28 HA HISH 2 -4.000 -0.781 1.098 >> ATOM 29 CB HISH 2 -2.516 -1.510 2.488 >> ATOM 30 HB1 HISH 2 -1.564 -1.990 2.400 >> ATOM 31 HB2 HISH 2 -2.494 -0.794 3.283 >> ATOM 32 CG HISH 2 -3.591 -2.538 2.747 >> ATOM 33 ND1 HISH 2 -3.867 -3.560 1.846 >> ATOM 34 HD1 HISH 2 -3.399 -3.715 0.964 >> ATOM 35 CD2 HISH 2 -4.447 -2.700 3.792 >> ATOM 36 HD2 HISH 2 -4.608 -2.157 4.723 >> ATOM 37 CE1 HISH 2 -4.846 -4.291 2.344 >> ATOM 38 HE1 HISH 2 -5.219 -5.152 1.791 >> ATOM 39 NE2 HISH 2 -5.203 -3.793 3.502 >> ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093 >> ATOM 41 C HISH 2 -2.329 0.595 1.164 >> ATOM 42 O HISH 2 -3.089 1.710 1.164 >> >> Thanks for any suggestions, >> >> Jose Tusell >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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