On 12/12/12 3:11 PM, James Starlight wrote:
Justin,
That errors was strange to me because I've already used Swiss's ITP
files for diffusional ligands including them in the topol.top of my
protein and there were no such errors about non-standart types in any
terms. It seems that some additions to the ffbonded.itp also required
besides the nonbonded.itp so the renaming Swiss's atoms to the CHARMM
would be less routinelly. I noticed some atoms types in the paper
which you provide me ( simulation in charmm22). Does the atom types
similar in both charmm fieds?
You probably don't get any errors because the .itp files provided to you from
the server include atomtype and bonded parameter definitions that are internally
self-consistent. What you're trying to do is use the "standard" CHARMM27 force
field with some new molecule that has no guarantee to be fully defined under the
existing force field.
CHARMM22 and CHARMM27 are the same for protein parameters, with the exception of
the introduction of CMAP in the latter.
Also I could not find any suitable example of CMAP for the long
molecule like my chromophore. I noticed that for amino acid typical
CMAP is the its backbone atoms as well as N and C atoms of 2 djacent
residues. So does the CMAP for chromophore consist of 2 strings like
below example or just one long strig ?
[ cmap ]
-C N CA1 C1 N2
CA2 C2 N3 CA3 C
The proper approach would be separate strings of 5 atoms.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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