RE: Query regarding parameter file generation of non standard residue

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Sep 08 2016 - 11:07:13 CDT

Please study the very informative FFTK tutorials. They show how the psf and parameter files are created and modified during the whole procedure.
Brian

________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Mahrukh Imtiaz [mahrukhimtiaz92_at_REMOVE_yahoo.com]
Sent: Thursday, September 08, 2016 9:01 AM
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Query regarding parameter file generation of non standard residue

Dear Abhi
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
<atyagiaa_at_connect.ust.hk> wrote:

Dear Mhrukh,

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

All the best

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Mahrukh Imtiaz <mahrukhimtiaz92_at_REMOVE_yahoo.com>
Sent: Thursday, September 8, 2016 5:54:35 PM
To: namd-l_at_ks.uiuc.edu
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 Imtiaz
COMSATS Islamabad, Pakistan

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