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biowerkzeug •TIP3P molecules included inside a cavity

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TIP3P molecules included inside a cavity

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TIP3P molecules included inside a cavity

Posted: Wed Aug 06, 2008 10:19 am
by ldav
I tried to include the water molecules (TIP3P) inside the active site of a target protein, but when running an MC simulation it crashed (segmentation fault). In fact all the parameters for OW-HW and HW-OW-HW were set to 0 in the file oplsaa_forcefield.dat. After correcting them I still got the same 'segmentation fault' error. But when I rewrote my own water molecule residue (WAT) it worked. So I guess something is going wrong with TIP3P.

Re: TIP3P molecules included inside a cavity

Posted: Thu Aug 07, 2008 2:40 pm
by martin
TIP3P water is hard coded for efficiency. It is not currently implemented for use with GB/SA. Your residue based water molecules is a good work around.
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