Dear Francois,
Thanks a lot for the detailed instructions with the PyRED usage and atom
types. I've submitted a new job with pre-defined atom types, and everything
looks ok. Now I am facing a new problem with the dihedral parameter of the
CA-CM=CM-CA. Theoretically, it should has two configurations, one is
"cis", and another is "trans". However, when I looked into the existed
dihedral parameter for CA-CM-CM-CA in frcmod.known, the only one could be
found is
CA-CM-CM-CA 1 6.65000000e+00 180.0 2. adapted from
parm99.dat i.e X-CM-CM-X 26.6/4
Maybe it is a dumb question, does that mean it only defined the "trans"
configuration? Should I worry about it? I've run two tests with two
different start configurations (cis and trans), but neither of them
transitioned to another.
Many thanks & Best regards,
Tao
2015-03-07 0:20 GMT+08:00 FyD <fyd.q4md-forcefieldtools.org>:
> Dear Tao,
>
> Yes I know we have to update our dictionary of atom types related to
> the CM vs CD atom types. We are correcting a series a limitation; On
> our todo list: we modify the web server, the PBS script and implement
> new features in PyRED almost every day...
>
> R.E.D. Server Dev. is saturated these days: we have to open more nodes
> also - uff...
>
> In your case:
> - Run a 1st PyRED job
> - Check the atom types as you did
> 1) if you like the generated atom types look for missing FF
> parameters (frcmod.unknown file)
> and use the 'Re_Fit mode to provide these missing FF parameters
> (frcmod.user file)
> i.e. http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
> -> END: ready to validate the FF generated by PyRED.
> 2) if you do not like the generated atom types
>
> grep MOLECULE1-ATMTYPE
> Data-R.E.D.Server/Data-Default-Proj/Project-out.config >>
> ./Project.config
> -> and modify the listed atom types according to what you think
>
> mv Mol_red1.pdb Mol_red1.pdb.origin (old atom order)
> cp Data-R.E.D.Server/Data-Default-Proj/Mol_red1-out.ent ./Mol_red1.pdb
> (to be sure to have a correct atom order; optimized geometry)
>
> rerun the job as you did the 1st time, check the atom types as you did
> again (should be ok this time) and look for missing FF parameters
>
> --
>
> in your case I would start by defining the CA atom types for all the
> sp2 carbon atoms in the two aromatic rings; and may be replace CD by
> CM for that double bond between these 2 rings...
>
> regards, Francois
>
>
> > Thanks a lot for providing such invaluable information. I've read the
> > tutorial and run two jobs on the R.E.D. Develoment server. However,
> > the atom typing of one looks a little strange, so I am looking for help
> for
> > this molecule (see attached picture).
> >
> > Generally, this molecule was two aromatic ring linked by ethylene. The
> > R.E.D server could correctly calculate the partial charge for it, but the
> > assigned atom types surprised me. The two carbon atom from ethylele was
> > assigned atom type "CD", which was mentioned in parm99.dat as "sp2 C atom
> > in the middle of: C=CD-CD=C". But, in our case, the two carbon atoms was
> > connected by double bond, not single bond. I also found the description
> of
> > "CD" from Wang et al. 2000, which said that,
> > "Considering that the inner two carbons of butadiene are not pure sp2
> > carbons, and the bond lengths between them are slightly longer than a
> pure
> > single Csp2?Csp2, a new atomic type (CD) can be introduced. "
> >
> > So, I am a little confused. Is CD the proper atom type for those two
> > carbons? Or do you have any experience/examples on such conjugated
> systems?
>
>
> > 2015-03-03 17:31 GMT+08:00 FyD <fyd.q4md-forcefieldtools.org>:
> >
> >> Dear Tao,
> >>
> >> See http://q4md-forcefieldtools.org/REDServer-Development/
> >> and its tutorial:
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
> >>
> >> and particularly:
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#17
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#18
> >>
> >> in agreement with:
> >> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
> >>
> >> regards, Francois
> >>
> >> > I am doing simulation on system that with various compounds bonded to
> the
> >> > N-terminal of certain peptide, like shown in the following picture.
> Now I
> >> > am facing the problems with creating unit for such N-Cap residue.
> >> >
> >> > ?
> >> > 1. Should I treat R1 combined R' as a N-Cap residue or just the R'
> only?
> >> > 2. In any case above, is there any method available to assign correct
> >> > partial charge and atom type for such non-standard residue?
>
>
>
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Received on Sun Mar 08 2015 - 01:00:02 PST
