[Chimera-users] Topology file creation

[Elaine Meng]

Hi Sankaran,

Chimera’s simulation setup does not include the glycosylation parameters (GLYCAM force field), so it is not recommended to create a topology file if you want a careful treatment of glycosylation.   Also, Chimera only writes topology files for AMBER, not other programs with different topology-file formats.

Although it might “work” (not fail with error messages) to simply run Dock Prep including hydrogen and charge addition, and then Write Prmtop to write the file for AMBER, the charges and other parameters  estimated for glycosylation groups would be rough, not the high quality of GLYCAM.  Dock Prep is in the menu under Tools… Structure Editing, and Write Prmtop is in the menu under Tools… Amber.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>

I found a tool for preparing glycoproteins with GLYCAM, but only for older versions of Amber, and I haven’t tried it: 
<http://glycam.org/old/AMBER/>

See also the Amber and Glycam websites
<http://ambermd.org/AmberModels.php>
<http://glycam.org/>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 16, 2018, at 9:27 AM, Sankaran SV . <119013033 at sastra.ac.in> wrote:
> 
> Hi users,
> Currently Iam working on protein glycosylation. Can anyone could give me a reference for topology file creation for running the simulation of glycosylated protein.
> -- 
> Sankaran.s.v