VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Mar 21 2014 - 14:18:07 CDT

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

On 03/21/2014 11:36 AM, Michael F. Harrach wrote:
> Dear all,
>
> I have a question about Impropers and psfgen.
>
> In the following a short explanation of what I did / want to do, then
> the actual question (marked by ACTUAL QUESTION)...
>
> I would like to generate isobutyric acid (or at least an
> approximation) for a series of simulations. Sadly, there does not seem
> to be a ready-made version available within the CHARMM force field
> files (if I am mistaken please correct me and skip the rest of the
> question), so I thought to try and combine parts of LEU and GLUP from
> the top_all22_prot.rtf topology file to make my own and use the
> appropriate parameters from par_all22_prot.prm...
>
> After looking through the topology tutorial
> (http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/)
> I then made some changes to the topology file and included "RESI IBA"
> in the file (see below), changing the name to
> "top_all22_prot_new.rtf". Obviously this will still need some tweeking
> but for the moment it is sufficient to get some sort of output with
> psfgen.
>
> I acquired the ideal and experimental coordinates from HIC-UP
> (http://xray.bmc.uu.se/hicup/ALQ/index.html) and gave the appropriate
> identification to the atoms as per my RESI IBA addition to the
> topology file (name: "HIC-UP_ideal_coordinates.pdb", see below).
>
> Then I used psfgen to generate a psf-file using the following script:
>
> package require psfgen
> topology top_all22_prot_new.rtf
> segment IBA {
> first none
> last none
> pdb HIC-UP_ideal_coordinates.pdb
> }
> guesscoord
> coordpdb HIC-UP_ideal_coordinates.pdb IBA
> writepdb output_IBA.pdb
> writepsf output_IBA.psf
>
>
>
> ACTUAL QUESTION:
>
> When looking at the resultant output I noticed that the psf-file does
> not contain any impropers, even though such are given in the internal
> coordinates of the topology file (eg. "IC CD1 CD2 *CG HG 1.5361
> 110.2600 120.0000 108.0200 1.1168").
> It makes sense to me that few dihedrals are given in the internal
> coordinates, given that they can be added on with auto dihedrals but I
> do not understand why the impropers are dropped. Is this standard? If
> so, why would be specified in the IC's? Or am I doing something
> completely wrong (in the context of creating the psf file at least
> otherwise I already have enough examples;-)
>
>
>
> Addition to the top_all22_prot.rtf file:
> RESI IBA 0.00 ! sollte Isobuttersäure ergeben
> GROUP
> ATOM CG CT1 -0.12 ! HD11 HD12
> ATOM HG HA 0.09 ! | /
> GROUP ! OE1 CD1--HD13
> ATOM CD1 CT3 -0.27 ! \\ /
> ATOM HD11 HA 0.09 ! CB-CG-HG
> ATOM HD12 HA 0.09 ! / \
> ATOM HD13 HA 0.09 ! HE2-OE2 CD2--HD23
> GROUP ! | \
> ATOM CD2 CT3 -0.27 ! HD21 HD22
> ATOM HD21 HA 0.09
> ATOM HD22 HA 0.09
> ATOM HD23 HA 0.09
> GROUP
> ATOM CB CD 0.75
> ATOM OE1 OB -0.55
> ATOM OE2 OH1 -0.61
> ATOM HE2 H 0.44
> BOND CD1 HD11 CD1 HD12 CD1 HD13 CD1 CG
> BOND CD2 HD21 CD2 HD22 CD2 HD23 CD2 CG
> BOND CG HG CG CB CB OE1 CB OE2
> BOND OE2 HE2
> DONOR HE2 OE2 ! habe das Ding zwar schon im BOND auftauchen, aber was
> solls - kommt ja in GLUP auch zweimal vor...
> IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168
> IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
> IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
> IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
> IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115
> IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360
> IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
> IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
> IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
>
> pdb file with ideal coordinates from HIC-UP with appropriate atom-names:
> REMARK HIC-UP ideal coordinates
> ATOM 1 CD1 IBA 1 1.016 -0.152 1.620 1.00
> 20.00 C+0
> ATOM 2 CG IBA 1 -0.194 -0.425 0.727 1.00
> 20.00 C+0
> ATOM 3 CD2 IBA 1 -1.381 0.413 1.206 1.00
> 20.00 C+0
> ATOM 4 CB IBA 1 0.137 -0.058 -0.695 1.00
> 20.00 C+0
> ATOM 5 OE1 IBA 1 1.231 0.376 -0.968 1.00
> 20.00 O+0
> ATOM 6 OE2 IBA 1 -0.781 -0.215 -1.661 1.00
> 20.00 O+0
> END
>
>
>