Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue

From: FyD <>
Date: Fri, 06 Mar 2015 17:20:06 +0100

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)
       -> END: ready to validate the FF generated by PyRED.
  2) if you do not like the generated atom types

Data-R.E.D.Server/Data-Default-Proj/Project-out.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 <>:
>> Dear Tao,
>> See
>> and its tutorial:
>> and particularly:
>> in agreement with:
>> 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
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