AMBER Archive (2003)

Subject: Re: AMBER: Carbohydrate connectivity

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 11 2003 - 10:09:08 CST

On Thu, Dec 11, 2003, Bimo Ario Tejo wrote:
>
> I'm trying to connect my protein with a sugar group. In PDB input
> file, I put the sugar group after C-terminal residue of the protein:
>
> ...
> ATOM 4019 CB VAL 520 59.503 65.879 -19.234 1.00 17.41
> ATOM 4020 CG1 VAL 520 58.356 64.987 -18.802 1.00 14.33
> ATOM 4021 CG2 VAL 520 60.675 65.007 -19.677 1.00 14.83
> ATOM 4022 OXT VAL 520 60.721 67.545 -21.929 1.00 17.00
> TER 4023 VAL 520
> HETATM 4024 C1 4NN 990 54.019 65.786 -2.071 1.00 27.09
> HETATM 4025 C2 4NN 990 53.098 67.012 -2.129 1.00 29.55
> HETATM 4026 C3 4NN 990 53.671 68.182 -2.907 1.00 28.87
> HETATM 4027 C4 4NN 990 55.155 68.370 -2.626 1.00 26.39
> HETATM 4028 C5 4NN 990 55.908 67.077 -2.730 1.00 24.89
> HETATM 4029 C6 4NN 990 57.387 67.254 -2.491 1.00 24.40
> ...
>
> Th sugar group should be attached with atom ND2 of residue 314
> (non-terminal residue), so I create a bond using xleap:
>
> bond lip.314.ND2 lib.10521.C1 (leap "renumbers" 990 as 10521)
>
> However, after I save the coordinate using "savepdb", a new
> bond has been created between C-terminal residue (Val-520) with C1
> atom of sugar group.

I don't understand you here: what tells you that this bond has been created?
(The pdb files created by LEaP do not contain connectivity information.)
The fact that leap renumbered the residue indicates that it recognized the
"TER" card, and hence put the sugar in a separate chain.

You can use the "desc" command to see what bonds are in the molecule; or
use rdparm on the output prmtop file. If you are using the pdb file you
saved to be read in later into LEaP, be sure to check that there is a TER
card after the protein part.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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