[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

James Starlight jmsstarlight at gmail.com
Fri Dec 14 20:28:09 CET 2012

Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
 No default Bond types

Its strange to me because chromophore itself consist of only one
uncommon bond  (in cyclized ring which could produce only several
additional angles and dihedrals)

By comparison in the case of Swiss atom names the total amount of the
same errors was only 9 (all erors about unknown dihedrals with
theadjacent residues. Although I've added capes in that model which
mimicks adjacent residues) it's difficult recognize suitable dihedral
Do you know any others attemps to simulate GFP with chromophore in
charmm with proof parameters ?


2012/12/12, Justin Lemkul <jalemkul at vt.edu>:
> 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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