[gmx-users] pdb2gmx(ver3.3) contain bug?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Apr 6 10:56:12 CEST 2006
Tomoshi Kameda wrote:
> Hi
>
>
> I'm going to simulate a HEME-Protein complex using GROMACS 3.3, and try
>
> pdb2gmx -f pdb1a6n.ent
>
> and select
> 0: GROMOS96 43a1 force field
>
>
> But, pdb2gmx cannot link FE(HEME) to NE2(HIS).
> pdb2gmx outputs
>
>> Opening library file /home/kameda/gromacs-3.3/share/top/specbond.dat
>> 5 out of 5 lines of specbond.dat converted succesfully
>> Special Atom Distance matrix:
>> HEME152 HEME152
>> FE1204 CAB1226
>> HEME152 CAB1226 0.565
>> HEME152 CAC1234 0.569 0.800
>
> ?????
>
> On trial, I type same command using version3.2.1, then output is
>
>> Opening library file /usr/local/share/gromacs/top/specbond.dat
>> 5 out of 5 lines of specbond.dat converted succesfully
>> Special Atom Distance matrix:
>> HIS12 HIS24 HIS36 HIS48 HIS64 HIS64 HIS81
>> NE2109 NE2199 NE2311 NE2430 NE2577 NE2578 NE2697
>> HIS24 NE2199 1.250
>> HIS36 NE2311 2.726 1.886
>> HIS48 NE2430 3.627 2.393 2.106
>> HIS64 NE2577 2.764 1.756 1.685 1.412
>> HIS64 NE2578 2.698 1.666 1.546 1.376 0.151
>> HIS81 NE2697 2.219 2.576 3.044 4.059 2.682 2.694
>> HIS82 NE2707 2.294 2.194 2.241 3.274 1.902 1.905 0.931
>> HIS93 NE2797 2.824 2.010 1.628 1.927 0.622 0.653 2.312
>> HIS97 NE2833 3.213 2.349 1.977 1.830 0.689 0.789 2.620
>> HIS113 NE2973 2.044 1.304 1.082 2.451 2.139 1.994 3.153
>> HIS116 NE21007 1.571 1.352 1.669 3.117 2.612 2.481 2.958
>> HIS116 NE21008 1.389 1.285 1.790 3.192 2.630 2.505 2.849
>> HIS119 NE21044 1.015 0.267 1.997 2.650 1.994 1.904 2.543
>> HEME152 FE1337 2.722 1.843 1.539 1.764 0.440 0.449 2.388
>> HEME152 CAB1359 2.255 1.512 1.325 2.115 0.865 0.806 2.024
>> HEME152 CAC1367 2.930 1.969 1.108 1.581 0.740 0.656 2.769
>> HIS82 HIS93 HIS97 HIS113 HIS116 HIS116 HIS119
>> NE2707 NE2797 NE2833 NE2973 NE21007 NE21008 NE21044
>> HIS93 NE2797 1.448
>> HIS97 NE2833 1.794 0.468
>> HIS113 NE2973 2.576 2.261 2.646
>> HIS116 NE21007 2.583 2.666 3.095 0.748
>> HIS116 NE21008 2.524 2.681 3.113 0.893 0.190
>> HIS119 NE21044 2.235 2.203 2.564 1.318 1.217 1.121
>> HEME152 FE1337 1.545 0.214 0.555 2.115 2.541 2.558 2.048
>> HEME152 CAB1359 1.199 0.626 1.082 1.760 2.076 2.078 1.668
>> HEME152 CAC1367 1.878 0.650 0.887 1.881 2.421 2.480 2.169
>> HEME152 HEME152
>> FE1337 CAB1359
>> HEME152 CAB1359 0.565
>> HEME152 CAC1367 0.569 0.800
>> Linking HIS-93 NE2-797 and HEME-152 FE-1337...
>
> and .top file shows the linkage, for example,
>
>> [atoms]
>> 926 NR 93 HIS1 NE2 388 -0.58 14.0067 ; qtot 1
>> 1521 FE 152 HEME FE 643 0.4 55.847 ; qtot 2.4
>> .......
>> [bonds]
>> .......
>> 926 1521 2
>
>
> The line '926 1521 2' does not exist in .top file made by GROMACS
> 3.3.
>
> For your information, there are not difference between
> /home/kameda/gromacs-3.3/share/top/specbond.dat
> with
> /usr/local/share/gromacs/top/specbond.dat.
>
>
>
> Is it caused by Bug ??
>
Not impossible. Please submit a bugzilla and upload the pdb file that
works in 3.2.1 and not in 3.3
>
> Thanks
>
> Tomoshi Kameda
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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