> On Dec 13, 2014, at 5:01 AM, Suman Chakrabarty <chakrabarty.suman.gmail.com> wrote:
>
> Dear all,
>
> I need to create topology and structure of some polypeptides with modified
> amino acids (mostly attached with sugar groups). I could successfully
> generate the GAFF parameters for the fragments, but I need your suggestions
> about tools that can create the 3D structures of polypeptides of such
> modified amino acids, preferably with controllable stereochemistry. I have
> been using GUI tools like Avogadro, but it becomes cumbersome to draw the
> whole chain and/or to be consistent in atom names and numbering while using
> them as fragments etc.
>
> Please advise me about the available tools (more convenient the better) to
> achieve this goal. Basically I need a general purpose tool to generate an
> arbitrary polymer structure given the monomer coordinates. It would be nice
> if the stereochemistry (D/L) of certain atoms could be controlled as well.
> Any guidance will be much appreciated. Thanks.
tleap can build chains of amino acids reasonably well using the “sequence” command. All of the amino acids in tleap are the L-enantiomer, but it is relatively straightforward to create the D-enantiomer instead if you want. All you have to do is reflect that residue in either the xy-, xz-, or yz-plane.
This is actually demonstrated in one of the tleap test suites. Have a look at $AMBERHOME/AmberTools/test/tleap/Run.cmds. In the first leap.in file that gets generated there, there is a section that says:
# Make a copy of GLU and reflect it in the xy-plane to create its stereoisomer,
# then create a capped version of that amino acid
dglu = copy GLU
transform dglu {{1 0 0} {0 1 0} {0 0 -1}}
d_amino = sequence {ACE dglu NME}
The resulting structure will be D-GLU (the copy command is used there to prevent the transformation from modifying the main GLU residue and thereby making all GLUs D).
There are probably better tools for doing this, but I’m not familiar with them.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 13 2014 - 07:30:03 PST
