I am not very experienced in Amber but here is what I do to add ACE
and NME from
the scratch.
1) Get the PDB
2)Add hydrogens
3)Load into xleap
4)xleap will add OXT terms to ends of chains
5) In adding NME, just remove the OXT oxygen and in that place, put the N
atom of NME (if adding a new atom, atom number is zero. Keep the residue
number as it is)
6) To add ACE groups, from each N terminal, remove two hydrogens bound to N
eg:- H1,H2 or H3
Then put the ACE carbon atom
7) Now load the file into xleap
There will be some messages about splitting residues because ACE and
the following amino acids as well as NME and the following amino acids both
have the same residue numbers
8)Some unknown hydrogens will be added into the residue after the ACE.
* First save the pdb with these added hydrogens
* Then remove those Hs from the pdb file and load the pdb file again
into xleap
Hope this helps
Thanx
Sajeewa Dewage
On Fri, May 11, 2012 at 9:40 AM, Albert <mailmd2011.gmail.com> wrote:
> Hi David:
> thank you very much for such kind comments. I've figured out we have
> to add ACE and NME into our PDB by ourselves and Amber can recognize
> them if the name is consist with chapter 'preparation for structure'
> mentioned in the manual.
>
> best
> Albert
>
> On 05/11/2012 01:52 PM, David A Case wrote:
> > Depends on what you want to do. Generally, MD simulations start from an
> > initial structure represented by a PDB file. As long as ACE and NME are
> in
> > the pdb file, you should be fine.
> >
> > ...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 Fri May 11 2012 - 08:30:05 PDT
