It's actually fairly easy if the following procedure is OK for you:
0) Make a copy of your starting PDB file since you're going to change it.
1) Locate the LYS that you want to mutate to an ARG in your starting PDB
file copy
2) Change the name LYS for every atom of that residue to ARG
3) Delete any atom that is unique to ARG that is not present in LYS
4) Rename any atom that is common to both, but named differently (and change
its name to what you find in ARG)
5) Run your new PDB file through leap the same way you did when you created
the initial topology file.
Leap fills in the missing atoms according to the library template. If you
are unsure about atom names, you can either take a look at the standard
amber amino acid library files ($AMBERHOME/dat/leap/lib/amino10.dat) or just
compare the atom names of other LYS/ARG residues in your starting PDB file.
This procedure is certainly scriptable, and it shouldn't take too long to do
so (unless part of your scripting process is learning how to use said
scripting language, in which case I'd argue it's time well spent ;) ).
HTH,
Jason
On Tue, Aug 9, 2011 at 4:48 PM, George A. Khoury <gkhoury.princeton.edu>wrote:
> Hello:
>
> I am new to amber and am trying to mutate a residue (LYS) to another
> residue
> (ARG). I have looked online and through the forums, and although there have
> been suggestions I could not find a sample listing of what commands to do
> to
> complete this procedure. It seems that the procedure is amenable to
> scripting-- if so, does someone have an example script for making mutations
> in AMBER, or a reference of how to make mutations within AMBER beyond those
> in the forums?
>
> Thank you in advance.
> Best regards,
> George
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 09 2011 - 14:30:14 PDT
