Re: Query regarding parameter file generation of non standard residue

From: Mahrukh Imtiaz (
Date: Thu Sep 08 2016 - 11:01:22 CDT

Dear AbhiI have tried that too but its not working because I have to generate parameters of this residue from scratch and fftk asks for already present parameter file or psf file, and I dont have both of them 

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  On Thu, Sep 8, 2016 at 4:37 PM, Abhishek TYAGI<> wrote: -- P {margin-top:0;margin-bottom:0;}
Dear Mhrukh,

Please try FFTK tool kit available in VMD, it will solve your problem.

All the best


Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of Mahrukh Imtiaz <>
Sent: Thursday, September 8, 2016 5:54:35 PM
Subject: namd-l: Query regarding parameter file generation of non standard residue 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 ImtiazCOMSATS Islamabad, Pakistan

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