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obminimize

bossarom

Hello Guys


Currently I'm writing my Bachelorthesis and therefor I'm using Openbabel for some calculations.


Now i have the following problems.


If i use: obminimize [-ff forcield] [-algorithm] <filname> to calculate the minimized energy of a given ligand a don't always get the same results. (of course I only compare results with the same ligande, same forcefield and same algorithm with each other)


For some ligands it works to get the same result if I use the command above to get the same result for the minimization.


But for most of the ligands the results are not reproducible. It also depends on the ligand which forcefields deliver reproducible results.


Thanks for your Help


Roman



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Re: obminimize

Geoff Hutchison
If i use: obminimize [-ff forcield] [-algorithm] <filname> to calculate the minimized energy of a given ligand a don't always get the same results. (of course I only compare results with the same ligande, same forcefield and same algorithm with each other)


I'm not quite sure I understand what you're doing. For many molecules, different starting geometries (even subtly different) can lead to different conformations - and thus different energies.

But for most of the ligands the results are not reproducible. It also depends on the ligand which forcefields deliver reproducible results.

Can you give us an example molecule and/or case of what you're trying to do?

Thanks very much,
-Geoff


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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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