Re: parameterizing a beta aminocyclohexanecarboxylic acid

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Oct 16 2007 - 12:47:51 CDT

Or perhaps someone on the CHARMM forum at www.charmm.org could help her with this? They've helped me in the past. Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 rwoodphd_at_yahoo.com ----- Original Message ---- From: Karol Kaszuba <karol.kaszuba_at_moskit.uwm.edu.pl> To: namd-l_at_ks.uiuc.edu Sent: Tuesday, October 16, 2007 9:46:31 AM Subject: Re: namd-l: parameterizing a beta aminocyclohexanecarboxylic acid Hello Rebeca, It will be the best to parametrize your molecule based on quantum chemistry software - GAMESS, GAUSSIAN. However if you do not have an ability to do it you can use parameters for similar connections specified in the CHARMM forcefield for example: in your acid you have a dihedral: C1-C2-N-H where: C1 is the carbon of non-aromatic ring C2 is the carbon of non-aromatic ring N - is a nitrogen atom to which two hydrogen atoms are bonded H - hydrogen atom bonded to your nitrogen You will not find (I was checking quickly so I could be wrong) a perfect equivalent of this type of dihedral in the CHARMM forcefield for proteins, but in the CHARMMM forcefield for Carbocyclic (Bicyclo[3.1.0]hexane) sugar analogs you will find a similar connection for CSAD (carbocyclic sugar with adenine base) H61 H62 \ / N6 look at the atoms named as a: C5 C6 N6 H61 | -> these COULD be your missing dihedral C6 // \ N1 C5--N7\\ | || C8-H8 C2 C4--N9/ / \\ / \ H2 N3 \ This same rule as above can be used for other missing parameters. Good luck! Regards, Karol ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/

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