AMBER Archive (2008)

Subject: Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri Nov 28 2008 - 17:34:43 CST

Thanks for your help but I want to acetylated at the side-chain of Ser
(see molecule below) not capping with ACE.

I think your example input file look fine so that I can adapt to the
acetylated-Ser. But how to delete HG and bond the atom C1 and OG after load
the following pdb file in tleap. Do you know how to do that ? (REMOVE and
BOND ?)

ATOM 1543 N SER A 200 7.759 65.944 57.010 1.00 0.00
ATOM 1544 CA SER A 200 7.487 64.752 57.832 1.00 0.00
ATOM 1545 CB SER A 200 7.094 65.144 59.263 1.00 0.00
ATOM 1546 OG SER A 200 5.706 65.323 59.454 1.00 0.00
ATOM 1547 C SER A 200 6.445 63.839 57.162 1.00 0.00
ATOM 1548 O SER A 200 6.735 63.311 56.097 1.00 0.00
ATOM 1549 CH3 ACE A 200 6.143 63.550 61.286 1.00 0.00
ATOM 1550 C1 ACE A 200 5.229 64.578 60.595 1.00 0.00
ATOM 1551 O1 ACE A 200 4.170 64.909 61.139 1.00 0.00

                    O1
                   //
Ser-- OG--- C1
                     \
                    CH3--H1
                    / \
                  H2 H3

Jitrayut
 2008/11/28 Guillermo Mulliert Carlín <Guillermo.Mulliert_at_lcm3b.uhp-nancy.fr
>

> 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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