Re: [AMBER] the question about the atom type of my molecule

From: Karl N. Kirschner <>
Date: Mon, 22 Jul 2013 11:03:42 +0200 (CEST)


  This is a tough one for assigning parm99SB atom types. I would guess that you will have missing parameters if you do this. It is also dependent upon how C36 is involved - does it have sp3 or sp2 hybridization?

  If I assume that C36 has sp3 hyrbidization (i.e. CT atom type), and if I were to use buta-1,3-diene as an analogue for the conjugated double bonds, then according to antechamber's assignment C13, C14, C33 and C35 would be CM, CD, CD, CM. This would then assign a small V2 term for the rotation about this bond. I would agree with you that C18 has a CT atom type, and C20 has a C atom type.

  Similarly, C13, C14, C33 and C35 would have c2, ce, ce, c2 atom types if you would use gaff atom types, while C18 and C20 would have c3 and c atom types.

  Since in is unclear as to which parm99SB atom types would best model the atoms in your system, the best thing to do would be to test the assigned bonded (ie. bond, angle, torsion) parameter's performance. I believe the Lennard-Jones parameters are all equivalent for sp2 carbon atoms.

Best regards,

----- Original Message -----
From: "lujing8556" <>
Sent: Monday, July 22, 2013 10:12:33 AM
Subject: [AMBER] the question about the atom type of my molecule

hi, everyone! can you help me to determine the types of C in the following molecule? I was puzzled for a long time. Thanks very much!

whether the C14, C13, C33 and C35 are CD or not?
whether the C18 is CT or not?
whether the C20 is C or not?

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Harbin Institute of Technology 
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Received on Mon Jul 22 2013 - 02:30:02 PDT
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