Re: [AMBER] Atom types for "alkene carbons", R.E.D.

From: FyD <>
Date: Thu, 28 Nov 2013 17:06:34 +0100

Dear Cecilia,

- First see
it is written:
"When describing the problem you encountered with R.E.D. Server,
please also provide the 'PXXXX' R.E.D. Server job name in the body of
your email so that we can more easily assist you."

- then if I look at three of your projects:
there is no atom type defined in the mol2 file generated.
well... this is 'normal' - if I dare to say that ;-) R.E.D. III.x and
R.E.D. IV (i.e. R.E.D. perl) does _not_ perform atom typing; atom
types have to be added using a LEaP script. See for instance projects
in R.E.DD.B.
  & its LEaP script were are defined the atom types...

- finally, instead of R.E.D. Server/R.E.D. IV simply use now R.E.D.
Server Dev./R.E.D. Python we released last week:

R.E.D. Python performs charge derivation, force field library
building, force field parameter generation, and far more....

in your case, prepare a PDB file; for instance use that generated by
R.E.D. Server/R.E.D. IV; for instance: Mol_m1-o1-qmra.pdb
(may be you could use more representative atom names!)
rename this file into Mol_red1.pdb & create an archive:
  tar zcvf archive.tgz Mol_red?.pdb
upload the archive at:

the idea is summarized at:

I hope this helps,
regards, Francois

> I am trying to obtain parameters for an alkene amide bond isostere
> using the R.E.D. server. My problem is at the very end of the
> procedure when trying to choose correct atom types for the two
> alkene carbons.
> I am using the force field amber99SB, and when checking the
> available atom types neither one of them seem correct. It is an sp2
> carbon, but it is not aromatic, a member of a ring or a carbonyl ...
> Are there no atom types for these carbons?

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Received on Thu Nov 28 2013 - 08:30:03 PST
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