David, thank you for your help
As I understood AmberTools also add missing atoms during loading of my pdb.
Also I have some questions about CAPing of the termi of my molecule
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
949 HH31 ACE 29 2.000 1.000 -0.000 1.00 0.00
ATOM 950 CH3 ACE 29 2.000 2.090 0.000 1.00 0.00
ATOM 951 HH32 ACE 29 1.486 2.454 0.890 1.00 0.00
ATOM 952 HH33 ACE 29 1.486 2.454 -0.890 1.00 0.00
ATOM 953 C ACE 29 3.427 2.641 -0.000 1.00 0.00
ATOM 954 O ACE 29 4.391 1.877 -0.000 1.00 0.00
ATOM 955 H7 ACE 29 3.582 3.629 -0.000 1.00 0.00
How I can edit that group to the standart form?
2) How I can place CAP groups to desired coordinates?
E.g if I use Edit- Unit Import Unit I can just import desired groups to my
pdb coordinates but how make linckage with N and C termi of my molecule ?
James
2011/11/1 David A Case <case.biomaps.rutgers.edu>
> On Tue, Nov 01, 2011, James Starlight wrote:
> >
> >
> > > Capping groups in Amber are called ACE (acetyl), NME (N-methyl) and NH2
> > > (NH_2). They are treated as regular amino acids, e.g. your sequence
> might
> > > be ACE-ALA-ALA-ALA-NME, for a tri-alanine helix with capping groups.
> > >
> > > So If my initial structure consist of only amino acids atoms could I
> build
> > CAPS via xleap or coordinates for this caps already must be in the
> initial
> > structure?
>
> You can use xleap, although it's a bit clunky as an interactive editor.
>
> > >
> > > So the problem is simple :) I havenot found how to save output in pdb
> :)
>
> See the "savePdb" command in LEaP.
>
> > So I needn't create addition functional groups for D isomers? Have they
> > already included in the param for instance leaprc.ff10?
>
> Yes. But I really encourage you to think about this carefully, and to
> understand why there is no force-field difference between D and L-amino
> acids. For example, try computing the energy of a L-amino acid, then the
> energy of its mirror image. Make this be something that you are confident
> you understand, not something you took my word for.
>
> ...dac
>
>
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Received on Wed Nov 02 2011 - 05:00:02 PDT
