[gmx-users] Prepping Docking Complexes

[Jack Shultz]

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?

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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)
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Workunit information
http://hydrogenathome.org/result.php?resultid=1412984

Original complex
http://hydrogenathome.org/sample_results/2559_1uwq_1238414317.pdb.tar.gz

-- 
Jack

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