AMBER Archive (2008)

Subject: RE: AMBER: A problem of dihedral angle

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 25 2008 - 10:48:56 CDT

Hi Harry,

 

The NPHIA means dihedrals not involving hydrogen, this is correct there are
6 CA-CA-CA-CA dihedrals.

The NPHIH means dihedrals involving hydrogen, in this case HA-CA-CA-HA and
HA-CA-CA-CA would be the proper ones and I believe there are 18 of these. 6
for HA-CA-CA-HA and 12 for the various HA-CA-CA-CA combinations. That leaves
6 remaining dihedrals which I believe are impropers on each CA atom to keep
the ring planar. So

 

        H

       /

CA---CA

       \

        \

         CA

 

Which would show up as an extra 6 dihedrals involving H giving you the 24
NPHIH dihedrals.

 

You can check this using rdparm. Have it load the prmtop file and then tell
it to printdihedrals and it will print out all the dihedral terms for you.
Impropers will be labelled with a B if I remember correctly.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Harry (Yicun) Ni
Sent: Wednesday, June 25, 2008 8:31 AM
To: amber_at_scripps.edu
Subject: AMBER: A problem of dihedral angle

 

Hello,

I'm using Amber to calculate the energy of benzene. In the output, there are
two parameters which are
'NPHIH=24' and 'NPHIA=6'. Does it mean that the total number of dihedral
angles in benzene is 30?
However, the program in our group for internal use shows that the total
number of dihedral angles in
benzene is 24. I counted manually and think 24 should be correct. (for every
C-C bond there are 4 dihedral
angles). So, could you help me on this problem? Also, could you tell me
which source files in Amber
generate the dihedral angles and assign the parameters? Thank you very much.

Harry @ ucf.chem

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