Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different

From: Xioling Chuang <xioling_c.hotmail.com>
Date: Tue, 3 Sep 2013 15:44:35 +0200

Dear Jason,

Thank you very much for your suggestions. If I would like to calculate using truncated normal mode estimation proposed by the Ryde group, how can I do?

Thank you,
Xioling


>
> My suggestion is to use the default values for drms (0.001) and maxcyc
> (10000). If snapshots don't converge, you should increase maxcyc, not
> decrease drms. If the normal mode calculations take too long, consider
> using either the quasi-harmonic approximation instead, or potentially look
> into the truncated normal mode estimation proposed by the Ryde group. [1]

                                               
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Received on Tue Sep 03 2013 - 07:00:02 PDT
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