From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Sep 08 2016 - 11:19:05 CDT
I also REALLY need to emphasize that in this particular case, the work has already been done. The glycosylation patch is already in the CHARMM force field, and you'd need a damn good reason to reparameterize it. I would expect any potential reviewer to be highly skeptical of a reparameterization like this.
On 09/08/2016 10:08 AM, Bennion, Brian wrote:
Please study the very informative FFTK tutorials. They show how the psf and parameter files are created and modified during the whole procedure.
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of Mahrukh Imtiaz [mahrukhimtiaz92_at_REMOVE_yahoo.com<mailto:mahrukhimtiaz92_at_REMOVE_yahoo.com>]
Sent: Thursday, September 08, 2016 9:01 AM
Subject: Re: namd-l: Query regarding parameter file generation of non standard residue
I 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
Please try FFTK tool kit available in VMD, it will solve your problem.
All the best
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu><mailto:owner-namd-l_at_ks.uiuc.edu> on behalf of Mahrukh Imtiaz <mahrukhimtiaz92_at_REMOVE_yahoo.com><mailto:mahrukhimtiaz92_at_REMOVE_yahoo.com>
Sent: Thursday, September 8, 2016 5:54:35 PM
Subject: namd-l: Query regarding parameter file generation of non standard residue
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.
COMSATS Islamabad, Pakistan
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