[gmx-users] diketopiperazine
Jose Tusell
jrta1981 at gmail.com
Fri Jan 22 23:05:54 CET 2010
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 <jalemkul at vt.edu> 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
>
> ========================================
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