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

James Starlight jmsstarlight at gmail.com
Sun Dec 16 06:52:07 CET 2012


It's not quite understood for me why such errors occurs in the atoms
of standard residues when I've bounded them to the C term of my
chromophore if the geometry of the adjacent residues might not be
changed. So it likely that some errors occur during parametrization of
the molecule which I could not identify ( In any case I'll be very
thankful for anyone who can provideme with some other version of the
integrated chromophore in charm for my future effort-on-errors :)
The main problems which I've forced in the improper group definition (
I've not recognize in the paper of simulation in charmm22 what groups
should define as improper although Swiss param produce the big set of
such groups- see below )

In addition It'll be very hardly to connect chromophore with adjacent
residues mainly due to definition of the addition dihedrals.

Finally Im not quite sure about CMAP definition ( I've used
C NH1 CT1 C NH1 1 24 24\
C NH1 CT1 C N 1 24 24\
in the CMAP.itp with the atom names of chromophore

C NH1 CT1 C NC=O 1 24 24\
C NC=O CR C=O N=C 1 24 24\
C=C C=O NC=O CR C=O 1 24 24\
C=O NH1 CT1 C NH1 1 24 24\

where NC=O and N=C types correspond to  the N and CR is the C-alpha atoms


2012/12/15, Justin Lemkul <jalemkul at vt.edu>:
> On 12/15/12 2:18 PM, James Starlight wrote:
>> So as I understood  it've happened because the conformation of the
>> adjacent residue is differ when that residue bounded to the
>> chromophore ( in comparison to the residue in unbound capped form).
> Conformation is irrelevant; atom types are all that matter here.
>> But in term of the backbone geometry of C and N-terms chromophore is
>> like a typical amino acid. Also Chromophore is defined as a protein in
>> the residue.dat.  When I've examined error log of my system I've
>> noticed that missing UB and dihedral parametrs of the i+1 residue have
>> never present in the ffbounded.itp ( the exact combination of the
>> triplet and quadruplet of atoms for UB and dihedral). Is there any
>> other ways to define termi of my non standard residue as the standard
>> one?
> If a particular bonded interaction is not present in the parent force field,
> you
> have to derive it parameters for it.
> -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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