Thank you for your kind help. But when I use rdparm and type the command
printDihedrals or dihedrals, it is said
"Segmentation fault" in both cases.Also, bonds and angles both give the same
error. Could you help me with this
problem? Thank you very much.
2008/6/25 Ross Walker <ross.rosswalker.co.uk>:
> 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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Harry (Yicun) Ni
> *Sent:* Wednesday, June 25, 2008 8:31 AM
> *To:* amber.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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Received on Sun Jun 29 2008 - 06:07:13 PDT
