[Chimera-users] GLYCAM force fields and Chimera

Eric Pettersen pett at cgl.ucsf.edu
Fri Dec 28 11:59:54 PST 2012

Hi John,
	In addition, Chimera does its force-field-based charge assignment by looking up the residue/atom names in a table.  The GLYCAM forcefield defines over 1400 residue names, most of which are not PDB standard residue names.  For instance, PDB residue VEA is a porphyrin, whereas in GLYCAM it is obviously a polysaccharide.  Therefore, the forcefield-based charge assignment mechanism in Chimera would have to be significantly reworked in order to properly support the GLYCAM files while still handling standard PDB residues that have names found in the GLYCAM files.  Even if this work was done, you (the user) would have to ensure that your structure used the proper GLYCAM residue and atom names rather than, e.g., GLC (PDB residue name for alpha-D-glucose) which is not found in the GLYCAM files!
	Doesn't seem like the payoff would be worth all the work...


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Dec 28, 2012, at 11:39 AM, Elaine Meng wrote:

> Hi John,
> Sorry, currently Glycam isn't included in the parameter lookup by Chimera.  Here are details on which parameter files are used for each of the force field choices:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations>
> You can assign charges manually, but it is more labor-intensive:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 26, 2012, at 11:27 PM, john Kerk wrote:
>> Dear Users 
>> I want to assign the partial charges of a glucose molecule using chimera-1.7 but I can not find this force field in Add charge suite although the GLYCAM force field files are existing under amber12.
>> can I get help
>> wishing merry Christmas ,
>> John
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> Chimera-users at cgl.ucsf.edu
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