On Wed, 2015-01-28 at 18:01 +0100, Mahad Gatti Iou wrote:
> Hello everyone,
>
> I'm new to AMBER, so I was reading other emails about the same topic as
> well as the user guide to start learning a little bit more.
> Basically, I want to run a simulation with NAMD using AMBER force field.
> Apparently it is not possible to use VMD's PSFgen plugin to obtain the
> parameter file, so I'm learning how to do that through leap.
> So far so good, I'm following a tutorial as well.
> When I'm loading the molecule I found this error, I got that there's some
> problem around the names of the residues in the PDB file and how AMBER
> actually reads them but still I wasn't able to find any information about
> what RU5 (and in general the syntax) is.
RU5 is the (old old old) residue name of a 5'-terminal ribouracil
residue. If that helps, great, but I suspect it doesn't.
> Can I receive some help regarding this matter?
Residue names in the PDB file *must* match the residue names in the
corresponding residue libraries (inside $AMBERHOME/dat/leap/lib). These
follow the PDB standard for the most part, but each protomer or tautomer
(e.g., protonated carboxylic acids, or epsilon- vs. delta-protonated
histidine) has a separate name which must be changed in the PDB file to
get the desired tautomer.
I would also suggest trying the "pdb4amber" tool, which should help
prepare your PDB file for use with leap.
For anything more than that, you will need to provide a lot more details
(with a lot more specificity) if you want help. Simplify the problem as
much as possible, then give exact input and output rather than trying to
describe it.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 28 2015 - 10:00:02 PST
