Another my question about XLEAP relate to the build-up missing residues in
my initial structure (e.g my iniial structure is the X-ray with the missing
residues)
As I've understood during loading of my pdb AmberTools always build missing
atoms like H-atoms. But could I also build missing residues ( e.g I could
obrtain list of such reidues in the hader of my pdb or manually)?
James
2011/11/2 David A Case <case.biomaps.rutgers.edu>
> On Wed, Nov 02, 2011, James Starlight wrote:
>
> > 1) I've found in that software ACE as well as other groups but they are
> not
> > standart
> >
> > e.g ACE is below instead of simple CH3 group
>
> I'm not sure what you think is "standard": ACE means an acetyl capping
> group,
> which is what you found. See tutorial B4 for some information about making
> libraries for things that are not already in the standard library.
>
> >
> > 2) How I can place CAP groups to desired coordinates?
>
> The "draw" command in xleap allows you to make interactive changes. Other
> graphical programs (many coming from the quantum chemistry world) are
> likely
> to be easier to use. Maybe people on the list can offer suggestions.
>
> ...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 Mon Nov 07 2011 - 05:00:02 PST
