Hi David,
Yes, as you guessed I will analyzing the data later in VMD, where I need to
perform various residue-based selections.
I just wondered if I can bypass the renumbering now than mapping the
numbers later.
Thanks for the options you provided. I will try them.
-Sundar
On Tue, Jan 23, 2018 at 2:14 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Jan 23, 2018, Sundar wrote:
> >
> > I am new to Amber and I have question on how to avoid atom renumbering
> when
> > using pdb4amber.
> > I couldn't find a clear answer to this in the amber mailing list
> archives.
> >
> > pdb4amber forces protein's atom numbering to start from 1. I certainly
> > don't want that.
>
> As its name implies, "pdb4amber" is designed to prepare pdb files for
> *Amber*,
> which internally always numbers atoms and residues starting at 1. It
> creates
> a "renum" file than can be used to map the original numbering scheme to
> the new
> one.
>
> If you don't want the renumbering to occur, then it seems likely(?) that
> you are
> planning to use the output for something else than feeding to Amber.
>
> So: there is no option to avoid the renumbering, since that is in many ways
> crucial to what pdb4amber is designed to do. There are a number of ways
> to reference the "original" residue numbers: see, e.g. the addPdb action
> in parmed, and the -ext flag in ambpdb.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 23 2018 - 13:00:02 PST
