Hello
On Fri, 28 Nov 2008, jitrayut jitonnom wrote:
|> Dear amber users,
|>
|> Is there anyone success in setting up a covalently bond between ligand and
|> enzyme with tleap or xleap ?
|> For example, If I want to make a acetylated serine how can I set up this
|> system.
you soulde create your new residue, with all the atoms, like this (well
my example is acetylated methionine)
ATOM 1 C1 ACE A 1 2.779 16.023 3.370 1.00 31.31 C
ATOM 2 O1 ACE A 1 2.503 15.263 2.399 1.00 44.36 O
ATOM 3 CH3 ACE A 1 1.802 17.070 3.818 1.00 36.07 C
ATOM 4 N MET A 1 3.731 15.587 4.153 1.00 37.41 N
ATOM 5 CA MET A 1 5.138 15.646 4.141 1.00 35.32 C
ATOM 6 C MET A 1 5.633 16.755 3.199 1.00 36.65 C
ATOM 7 O MET A 1 5.247 17.091 2.090 1.00 38.17 O
ATOM 8 CB MET A 1 5.948 14.392 4.107 1.00 41.69 C
ATOM 9 CG MET A 1 5.190 13.146 4.444 1.00 48.68 C
ATOM 10 SD MET A 1 5.671 12.457 6.047 1.00 38.49 S
ATOM 11 CE MET A 1 5.513 10.705 5.729 1.00 15.99 C
add hydrogens, and calculate charges with antechamer (if you with you
can use gaussain first). I do not know if you are using ambertools 1.2, but
maybe give in your tleap file all the links between atoms.
Hope this help
Guillermo Mulliert
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Received on Fri Dec 05 2008 - 18:03:27 PST
