Thanks Justin, I used specbond.dat with a 0.15nm searching distance to create the bond, it seemed to work.<br><br>Ramon<br><br><div class="gmail_quote">On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Jose Tusell wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
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:<br>
<br>
</blockquote>
<br></div>
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."<br>
<br>
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.<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
specbond.dat<br>
8<br>
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2<br>
CYS SG 1 HEME FE 2 0.25 CYS2 HEME<br>
CYS SG 1 HEME CAB 1 0.18 CYS2 HEME<br>
CYS SG 1 HEME CAC 1 0.18 CYS2 HEME<br>
HIS NE2 1 HEME FE 1 0.2 HIS1 HEME<br>
MET SD 1 HEME FE 1 0.24 MET HEME<br>
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2<br>
TRP N 1 HISH C 1 0.2 TRP HISH<br>
<br>
whdikp.pdb<br>
REMARK S 14 x 14 mn oif<br>
ATOM 1 N TRP 1 -0.813 0.594 1.164<br>
ATOM 2 H TRP 1 -0.249 1.064 1.843<br>
ATOM 3 CA TRP 1 -0.264 -0.210 0.004<br>
ATOM 4 HA TRP 1 0.855 -0.244 0.066<br>
ATOM 5 CB TRP 1 -0.633 0.484 -1.321<br>
ATOM 6 HB1 TRP 1 -1.672 0.344 -1.531<br>
ATOM 7 HB2 TRP 1 -0.408 1.528 -1.262<br>
ATOM 8 CG TRP 1 0.205 -0.166 -2.397<br>
ATOM 9 CD1 TRP 1 0.227 -1.464 -2.727<br>
ATOM 10 HD1 TRP 1 -0.407 -2.173 -2.195<br>
ATOM 11 CD2 TRP 1 1.119 0.455 -3.258<br>
ATOM 12 NE1 TRP 1 1.166 -1.607 -3.796<br>
ATOM 13 HE1 TRP 1 1.401 -2.473 -4.259<br>
ATOM 14 CE2 TRP 1 1.673 -0.432 -4.078<br>
ATOM 15 CE3 TRP 1 1.485 1.803 -3.344<br>
ATOM 16 HE3 TRP 1 1.065 2.575 -2.699<br>
ATOM 17 CZ2 TRP 1 2.626 -0.117 -5.054<br>
ATOM 18 HZ2 TRP 1 3.035 -0.902 -5.690<br>
ATOM 19 CZ3 TRP 1 2.444 2.145 -4.320<br>
ATOM 20 HZ3 TRP 1 2.741 3.190 -4.402<br>
ATOM 21 CH2 TRP 1 2.990 1.222 -5.140<br>
ATOM 22 HH2 TRP 1 3.727 1.540 -5.878<br>
ATOM 23 C TRP 1 -0.816 -1.621 0.004<br>
ATOM 24 O TRP 1 -0.072 -2.712 0.004<br>
ATOM 25 N HISH 2 -2.331 -1.621 0.004<br>
ATOM 26 H HISH 2 -2.895 -2.093 -0.674<br>
ATOM 27 CA HISH 2 -2.881 -0.816 1.162<br>
ATOM 28 HA HISH 2 -4.000 -0.781 1.098<br>
ATOM 29 CB HISH 2 -2.516 -1.510 2.488<br>
ATOM 30 HB1 HISH 2 -1.564 -1.990 2.400<br>
ATOM 31 HB2 HISH 2 -2.494 -0.794 3.283<br>
ATOM 32 CG HISH 2 -3.591 -2.538 2.747<br>
ATOM 33 ND1 HISH 2 -3.867 -3.560 1.846<br>
ATOM 34 HD1 HISH 2 -3.399 -3.715 0.964<br>
ATOM 35 CD2 HISH 2 -4.447 -2.700 3.792<br>
ATOM 36 HD2 HISH 2 -4.608 -2.157 4.723<br>
ATOM 37 CE1 HISH 2 -4.846 -4.291 2.344<br>
ATOM 38 HE1 HISH 2 -5.219 -5.152 1.791<br>
ATOM 39 NE2 HISH 2 -5.203 -3.793 3.502<br>
ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093<br>
ATOM 41 C HISH 2 -2.329 0.595 1.164<br>
ATOM 42 O HISH 2 -3.089 1.710 1.164<br>
<br>
Thanks for any suggestions,<br>
<br>
Jose Tusell<br>
<br>
</blockquote>
<br></div></div><div><div></div><div class="h5">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>