On 3 December 2012 04:16, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Dec 03, 2012, Thomas Evangelidis wrote:
> >
> > I want to create .prmtop and .inpcrd files for a protein/retro-inverso
> > peptide complex. I've read in older posts that there is no need to modify
> > any amber99sb (or its variants) library to include D-amino acids.
> However,
> > when I use regular amino acid names for the D- amino acids in the pdb
> file
> > I get errors like:
> >
> > FATAL: Atom .R<NASN 1>.A<HB1 19> does not have a type.
>
> You don't say how you created your input pdb file, but it looks like it is
> using the "old" (pdb version 2) atom names. I think you can get "reduce"
> to
> update the names, or protonate can do it. If there are just a few D-amino
> acids, you might even rename by hand.
>
> I made it with the D_SwissSidechain_chimera p;lu
http://swisssidechain.ch/visualization/chimera.html
You were right. It was a naming conflict. I fixed it with MOLPROBITY
(reduce and protonator did not change the atom names).
Thanks,
Thomas
>
> > and warnings like:
> >
> > WARNING: There is a bond of 4.673348 angstroms between:
> > ------- .R<NASN 1>.A<C 15> and .R<GLU 2>.A<N 1>
>
> This is a pretty straightforward message: if you indeed have such a long
> peptide bond in the PDB file, you need to address the question of how it
> got
> there.
>
> ....dac
>
>
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--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Fri Dec 07 2012 - 08:30:02 PST
