AMBER Archive (2008)

Subject: Re: AMBER: connectivity lose during the minimizations

From: David A. Case (case_at_scripps.edu)
Date: Sat Jan 12 2008 - 14:28:37 CST

On Sat, Jan 12, 2008, rams rams wrote:
>
> 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 ?

You will need to provide detailed information about what you did. For
example, how did you create the library file for the inhibitor? How are you
deciding whether the "connectivity" is present or absent?, etc.

Generally, make sure that you can minimize the inhibitor all by itself first.
But without more information about what you actualy did (you can just say
"generated during LEaP") no one will really be able to help.

...dac

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