[gmx-users] Prepping Docking Complexes
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 30 19:20:24 CEST 2009
Jack Shultz wrote:
> Hi Guys,
>
> Thanks for previous help. Especially Justin. I got the amber03 and
> tip3 water models working through my BOINC project now. But if I want
> to simulate a docking complex, I'm running to some errors preparing
> it. I have not done extensive research on this yet, but I'm wondering
> how I can prep these ligand-receptor complexes so they are acceptable
> to pdb2gmx. Maybe someone can point me in the right direction?
>
> -------------------------------------------------------
> Program pdb2gmx_d, VERSION 4.0.3
> Source code file: pdb2gmx.c, line: 893
>
> Fatal error:
> Chain identifier 'B' was used in two non-sequential blocks (residue
> 975, atom 7970)
> -------------------------------------------------------
>
That means you've split apart chain B. If you look at your structure file,
you'll find:
ATOM 7934 NE2 HIS B 489 126.270 67.930 67.564 1.00 47.43 -0.221 NA
ATOM 7935 OXT HIS B 489 132.243 66.924 65.753 1.00 43.53 -0.646 OA
HETATM 7937 C ACT B1490 116.586 88.801 86.875 1.00 67.39 0.186 C
HETATM 7938 O ACT B1490 115.409 88.588 86.537 1.00 67.73 -0.647 OA
HETATM 7939 OXT ACT B1490 117.292 89.696 86.359 1.00 67.35 -0.647 OA
HETATM 7940 CH3 ACT B1490 117.160 87.930 87.956 1.00 67.32 0.109 C
TER 7941 ACT B1490
ATOM 1 O1 0.0 d 000 125.675 63.107 72.217 0.00 0.00 -0.348 OA
ATOM 2 C1 0.0 d 000 125.252 63.738 73.407 0.00 0.00 0.292 C
ATOM 3 O3 0.0 d 000 124.554 64.931 73.121 0.00 0.00 -0.348 OA
ATOM 4 C4 0.0 d 000 124.318 65.780 74.249 0.00 0.00 0.179 C
ATOM 5 C6 0.0 d 000 123.970 64.972 75.543 0.00 0.00 0.180 C
ATOM 6 C7 0.0 d 000 123.396 63.571 75.233 0.00 0.00 0.183 C
ATOM 7 C8 0.0 d 000 124.363 62.784 74.308 0.00 0.00 0.204 C
ATOM 8 C5 0.0 d 000 125.509 66.741 74.382 0.00 0.00 0.198 C
ATOM 9 O4 0.0 d 000 126.073 66.914 73.114 0.00 0.00 -0.398 OA
ATOM 10 H8 0.0 d 000 125.582 66.394 72.473 0.00 0.00 0.209 HD
ATOM 11 O5 0.0 d 000 125.109 64.795 76.367 0.00 0.00 -0.390 OA
ATOM 12 H9 0.0 d 000 124.827 64.626 77.270 0.00 0.00 0.210 HD
ATOM 13 O7 0.0 d 000 122.126 63.780 74.623 0.00 0.00 -0.390 OA
ATOM 14 H14 0.0 d 000 122.027 63.183 73.878 0.00 0.00 0.210 HD
ATOM 15 O6 0.0 d 000 123.684 61.791 73.545 0.00 0.00 -0.388 OA
ATOM 16 H13 0.0 d 000 124.232 61.529 72.802 0.00 0.00 0.210 HD
ATOM 17 C2 0.0 d 000 125.085 63.646 71.046 0.00 0.00 0.187 C
ATOM 18 C3 0.0 d 000 123.849 62.820 70.568 0.00 0.00 0.183 C
ATOM 19 C12 0.0 d 000 123.639 62.990 69.062 0.00 0.00 0.204 C
ATOM 20 C11 0.0 d 000 124.937 62.624 68.251 0.00 0.00 0.288 C
ATOM 21 O10 0.0 d 000 126.135 62.786 69.012 0.00 0.00 -0.349 OA
ATOM 22 C10 0.0 d 000 126.147 63.869 69.925 0.00 0.00 0.180 C
ATOM 23 O2 0.0 d 000 124.007 61.412 70.818 0.00 0.00 -0.390 OA
ATOM 24 H4 0.0 d 000 124.394 60.991 70.048 0.00 0.00 0.210 HD
ATOM 25 O11 0.0 d 000 123.229 64.326 68.826 0.00 0.00 -0.388 OA
ATOM 26 H22 0.0 d 000 123.738 64.694 68.100 0.00 0.00 0.210 HD
ATOM 27 O9 0.0 d 000 125.021 63.316 67.003 0.00 0.00 -0.369 OA
ATOM 28 H19 0.0 d 000 125.159 62.682 66.295 0.00 0.00 0.212 HD
ATOM 29 C9 0.0 d 000 127.585 64.061 70.409 0.00 0.00 0.198 C
ATOM 30 O8 0.0 d 000 128.253 62.824 70.315 0.00 0.00 -0.398 OA
ATOM 31 H15 0.0 d 000 127.660 62.167 69.944 0.00 0.00 0.209 HD
OA^M
ATOM 7873 CB PRO B 482 123.510 77.736 70.316 1.00 27.76 0.034 C ^M
ATOM 7874 CG PRO B 482 124.070 78.915 71.107 1.00 27.76 0.027 C ^M
Chains need to be continuous, so don't insert molecules within other molecules!
-Justin
> Workunit information
> http://hydrogenathome.org/result.php?resultid=1412984
>
> Original complex
> http://hydrogenathome.org/sample_results/2559_1uwq_1238414317.pdb.tar.gz
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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