[AMBER] free energy calculation: turn off the VDW interaction between ligand and protein

From: Bing Xiong <bxiong.mail.shcnc.ac.cn>
Date: Sat, 31 Dec 2011 08:42:17 +0800

Dear all,
Happy new year!

By reading the manual (amber 10), the softcore part stated that we
can turn off the charge with crgmask. Can we turn off the vdw interaction of
 ligand with protein as commonly used in double decouping
calculations? how to do this in amber? such as how to prepare the V1 state(V0 is the vdw interaction on, charge=0.0 )? is there any parameter like crgmask for turn off the VDW interaction?

Best regards,


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Received on Fri Dec 30 2011 - 17:00:02 PST
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