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 Fri Mar 06 2015 - 08:30:02 PST
