[AMBER] R.E.D, alkene isostere, Gly-Pro, P9501

From: Cecilia Lindgren <cecilia.lindgren.chem.umu.se>
Date: Thu, 9 Jan 2014 11:28:40 +0100

Dear Sir/Madame,

I am trying to calculate charges for an alkene amide bond isostere for the dipeptide fragment Gly-Pro. By analogy I added the following information in a frcmod.user file:

CM-CA-CT 70.0 119.70 Source (from CM-CM-CT)
CT-CA-CT 50.0 118.00 Source (from CT-N-CT)
CA-CM-CT 70.0 119.70 Source (from CM-CM-CT)
C-CT-CA 63.0 110.10 Source (from C-CT-N)
CM-CT-N 63.0 110.10 Source (from C-CT-N)

CM-CT-CA-CT 1.0 180.0 2 Source

My question is: what information would you recommend that I use for IMPROPER: CM-CT-CA-CT? Here I have based it on C-CM-N*-CT, but I am not convinced that it is ok, but I have not found any other that I like better either... I am using amber99sb.

Best regards,

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Received on Thu Jan 09 2014 - 02:30:02 PST
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