AMBER Archive (2004)

Subject: AMBER: how to correct the charge of oligosaccharides

From: Wen-Chi Tseng (tsengwc_at_ch.ntust.edu.tw)
Date: Mon Aug 09 2004 - 21:28:25 CDT

Hi,

I used glycam04 to build three oligos.Then, I checked these
structures, and got the following messages.

> x = sequence {OME 1GA 4GA}
> y = sequence {OME 1GA 4GA}
> z = sequence {OME 1GA 4GA 4GA}
> check x
Checking 'x'....
Warning: Close contact of 0.755725 angstroms between .R<OME 1>.A<
...
check: Warnings: 3
Unit is OK.
> check y
Checking 'y'....
Warning: Close contact of 0.755725 angstroms between .R<OME 1>.A<
...
check: Warnings: 5
Unit is OK.
> check z
Checking 'z'....
ERROR: The unperturbed charge of the unit: 0.011000 is not integral.
WARNING: The unperturbed charge of the unit: 0.011000 is not zero
...
There are missing parameters.
check: Errors: 1 Warnings: 13
> charge x
Total unperturbed charge: 0.0050
Total perturbed charge: 0.0050
> charge y
Total unperturbed charge: 0.0080
Total perturbed charge: 0.0080
> charge z
Total unperturbed charge: 0.0110
Total perturbed charge: 0.0110

The total charge seemed to increase when the monomer number
increased. Can anyone suggest how to balance the total charge of a
long, linear polysaccharide?

I also saved these oligos in pdb file, and used vmd, swiss-pdbViewer,
and xleap to visualize the molecules. These structures could be seen
correctly only under xleap. Under vmd and spdbv, incorrect linkages
were found. Does anyone know how to fix this?

regards,

Wenchi
   

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