VMD-L Mailing List

From: Michael F. Harrach (harrach_at_fkp.tu-darmstadt.de)
Date: Mon Mar 24 2014 - 03:48:36 CDT

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