[gmx-users] update .hdb file

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Sat Apr 9 19:39:26 CEST 2016

Hello Shahla, 

We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table file for you with any rtp file. Please contact me contact me off list if you are interested



Message: 5
Date: Sat, 9 Apr 2016 08:49:05 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, Shahla Omidi <a.omidi at shirazu.ac.ir>
Subject: Re: [gmx-users] update .hdb file
Message-ID: <5708FA41.2060607 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 4/9/16 1:55 AM, Shahla Omidi wrote:
> ?Hi
> I want to simulate a glycoprotein, I have defined a new residue with charmm36
> inorder to update the .hdb file, I need to define the order of atoms that are conecting to atoms that is conecting to H atoms in my new residue
> but I dont exactly know about the standard format of showing atoms connection to   atoms.
> Is the order of them relate to their distance from the n terminal or is another standard to show which connected should come first?
> for example:
> HB  CB  CG  CA
> and
> HB  CB  CA   CG
> which one is true?

Read the manual, section 5.7.4.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441



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