On 12/16/12 12:52 AM, James Starlight wrote:
Justin,
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
Ignore geometry. Focus on atom types. Bonded interactions are assigned based
on what atom types are used for the atoms involved. Their names, coordinates,
and all that other stuff are irrelevant for the purposes of pdb2gmx.
This email thread has gone on for dozens of messages now, all with basically the
same problem - so you need to isolate your focus. It doesn't matter if you're
getting two errors or a hundred; work one-by-one to identify each offending
interaction type and determine what might be causing it. There's nothing
"standard" about what you're trying to do, and there is no guarantee that there
are bonded parameters built-in for the types of interactions you're looking for.
In theory, the topology obtained from Swiss-Param should have everything you
need in one form or another, such that parameters can be added in, if needed.
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 :)
Surely a search of the literature would turn up people who have simulated GFP
using Gromacs, no? Contacting their corresponding author(s) is probably a very
efficient means to establishing what others have done.
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 )
Any planar group (peptide bond, aromatic ring, etc) should be assigned an
improper. These are described in the manual.
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
Again, names are irrelevant. Only the types matter. Note that each CMAP entry
corresponds to a huge sequence of numbers (note that '\' is a line continuation
character), so I'm not sure what you're trying to do in the cmap.itp file. If
deriving CMAP parameters becomes prohibitive, you may need to consider a
different force field, though all of the atoms involved should be in the backbone.
-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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