VMD-L Mailing List

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

  _____

Institute for Molecular Bioscience
The University of Queensland
Building 80, Services Road
St Lucia
Queensland 4059
Australia

Phone: +61 (0)413 165 805
Email: <mailto:j.swedberg_at_imb.uq.edu.au> j.swedberg_at_imb.uq.edu.au

 <http://www.ihbi.qut.edu.au/> http://www.imb.uq.edu.au/

Description: Description: imb-logo

  _____

 "Important: This transmission is intended only for the use of the addressee
and may contain confidential or legally privileged information. If you are
not the intended recipient, please contact the sender immediately."

 


image001.jpg