VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Mar 24 2014 - 11:13:55 CDT

Hi Michael,

That was a detail I was unaware of (since for the most part the IC
entries can be ignored 99% of the time), so we are both talking about
CHARMM. Again, IC table entries are only there to help guess coordinates
when they are missing. For your molecule, there should be an improper on
the carboxylic acid carbon, which keeps it in the plane, but that's it.
Don't worry so much about the IC table. You already have an optimized
geometry, so there are no atoms left to guess, and so the IC table
doesn't add any information.
-Josh Vermaas

On 03/24/2014 03:48 AM, Michael F. Harrach wrote:
> Dear Josh,
>
> thanks for your answer! I will definitely take a look at
> "https://cgenff.paramchem.org/". I am slightly surprised though
> concerning the intercal coordinates. I looked through the
> topology-tutorial
> "http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/",
> where the topology files are explained, with a part concerning the IC's:
>
> http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html#SECTION00041000000000000000
>
> and it is stated in the text: "The * next to the C atom indicates that
> it is at the center of an improper angle definition. No * indicates
> that the 4 atoms do not have an improper topology." with two examples
> being given two explain how the IC's work:
>
> * IC A B C D [bond(AB)] [angle(ABC)] [dihedral(ABCD)] [angle(BCD)]
> [bond(CD)]
> * IC A B *C D [bond(AC)] [angle(BCA)] [improper(ABCD)] [angle(BCD)]
> [bond(CD)].
>
> Concerning "IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996"
> they then state "...atoms C, CA, N, and HN have a 180.0000$^\circ$
> improper angle...".
> I do not quite understand how this meshes with what you said. As far
> as I understand the tutorial references the CHARMM force field.
> Perhaps we are talking about topology files to different force fields?
>
> Sincerely,
> Michael
>
>
>
> > Hi Michael,
> > An IC table entry isn't an improper definition. Lines beginning with IC
> > in a topology file are there to help psfgen or charmm guess where to
> > place atoms based on the position of existing atoms. For the line you
> > showed:
> >
> > IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168
> >
> > This should be read as the bond between CD1 and CD2 in this residue
> > should be 1.5361 Angstroms, the angle between CD1 CD2 *CG HG should be
> > 110.26 degrees, the dihedral angle for the torsion described by the 4
> > atoms should be 120 degrees, the angle formed by the last three atoms
> > should be 108.02 degrees, and the bond between the last two atoms should
> > be 1.1168 Angstroms.
> >
> > If you were to have an improper, the definition of it would be something
> > like:
> >
> > IMPR N -C CA HN C CA +N O
> >
> > which are commonly seen in protein topology files to keep the backbone
> > nitrogen and carbonyl carbon "flat", and represents two improper terms.
> >
> > Combining parts of different residues together can be complicated, and
> > result in terms missing from the force field if you aren't careful. As a
> > double check against your own work, you may want to use the ParamChem
> > webserver (https://cgenff.paramchem.org/), which automates
> > parameterization by analogy using just an input pdb. It will also
> > attempt to guess at how poor the analogy model is, although quickly
> > looking at your structure, I think cGenFF will handle it just fine.
> > -Josh Vermaas
>
>