From: Joakim Swedberg (j.swedberg_at_imb.uq.edu.au)
Date: Wed May 02 2012 - 19:20:41 CDT

Dear all,

I need to simulate N-methylated amino acids. Is there anybody out there that
have tried? I used the website http://www.charmming.org/charmming/ to get
the most of the values for the topology (see below) and parameters. When I
run the simulation the peptide bond and the C1 carbon appears fine while
hydrogen's of the NMe group spin around. Any ideas would be appreciated

 

 

PRES NME 0.00

GROUP

ATOM N NH1 -0.32 !

ATOM C1 CT3 -0.09 !

ATOM H11 HA 0.09 !

ATOM H12 HA 0.09 !

ATOM H13 HA 0.09 !

ATOM CA CT1 0.05 !

ATOM HA HB 0.09 !

DELETE ATOM HN

DELETE BOND N HN

DELETE DONOR HN N

BOND C1 N H11 C1 H12 C1 H13 C1

DELETE IMPR N -C CA HN

DELETE IC -C CA *N HN

IMPR N -C CA C1

ANGLE H11 C1 N H12 C1 N H13 C1 N

DIHE H11 C1 N CA H12 C1 N CA H13 C1 N CA

DIHE H11 C1 N -C H12 C1 N -C H13 C1 N -C

IC -C CA *N C1 1.361 124.3700 180.0000 114.1800 1.466

IC H11 N *C1 H12 1.1109 109.6000 119.1300 111.0500 1.1119

IC H11 N *C1 H13 1.1109 109.6000 -119.5800 111.6100 1.1114

 

Joakim Swedberg
BSc (Honours) PhD

Research Officer

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