AMBER Archive (2008)

Subject: AMBER: connectivity lose during the minimizations

From: rams rams (
Date: Sat Jan 12 2008 - 05:40:21 CST

Dear All,

I am doing a gasphase minimization of my protein along with an inhibitor.
The PDB generated during the LEaP is alright (I mean the connectivity among
the inhibitor atoms are remained the same as the crystal structure). During
the gasphase minimizations, the connectivity of a few of the atoms in
inhibitor are losing though i am keeping high restraint force on the
inhibitor. Also, despite of the restraint, the bond distances are also
varying much. Can any one explain to me how to keep the bonds of the
inhibitor intact ?

Thanks and Regards,

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