Dear nirmal,
try prodrg server for generating the topology file for
the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/
________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Nirmal Prasad [nimmynir...@gmail.com]
Sent: Wednesday, January 11, 2012 9:45 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] HEME topology
Hello,
Can any one send topology for Heme group..My work is stuckeup
here are the PDB parameters for HEME
-------------------------------------------------------------------------------
HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00
HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00
HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00
HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00
HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00
HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00
HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00
HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00
HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00
HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00
HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00
HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00
HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00
HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00
HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00
HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00
HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00
HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00
HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00
HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00
HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00
HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00
HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00
HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00
HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00
HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00
HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00
HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00
HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00
HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00
HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00
HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00
HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00
HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00
HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00
HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00
HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00
HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00
HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00
HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00
HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00
HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00
HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00
TER 3894 HEM 482
--------------------------------------------------------------------------------
thanks in advance
nirmal
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