VMD-L Mailing List

From: Michael F. Harrach (harrach_at_fkp.tu-darmstadt.de)
Date: Fri Mar 21 2014 - 11:36:31 CDT

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