Re: Query regarding parameter file generation of a non standard residue

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Sep 07 2016 - 16:49:15 CDT

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Hi Mahrukh,

Look in the stream files, specifically toppar_all36_carb_glycopeptide.str. N-glycoslyation is common enough that it has already been parameterized (NGLB or NGLA, depending on the linkage to the sugar).

-Josh

On 09/07/2016 02:17 PM, Mahrukh Imtiaz wrote:
Dear all,

I am currently facing some problems in generating a Charmm parameter file for a non standard amino acid i.e. Glucose attached to Asparagine (N-glycosylation). I have generated an optimized structure of this non standard residue via Gaussian and determined the bond, angle and dihedral constraints. However, I am unable to calculate the force constant value for above mentioned constraints. Any help regarding this issue would be highly appreciated as I am new at parameters generation.

Best regards,
Mahrukh Imtiaz
COMSATS Islamabad, Pakistan

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