[gmx-users] HYL force field

Justin Lemkul jalemkul at vt.edu
Mon May 11 13:41:53 CEST 2015

On 5/10/15 10:12 PM, Ming Tang wrote:
> Hi, 范聪
> I have never worked with ligand, and will try to learn this tutorial.

I think you need to define what "containing" means - is it a constituent residue 
of the protein sequence or is it a noncovalently bound ligand?  The approach in 
both cases differs.  For the former, you need to create an .rtp entry and 
process the chain with pdb2gmx.  For the latter, you need to generate a separate 
topology for the bound ligand.

The proper method for parametrizing the ligand depends on the force field you 
want to use.


> Thanks.
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of ??
> Sent: Monday, 11 May 2015 11:03 AM
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] HYL force field
> Hello, can you treat HYL as ligand and build its forcefield parameters referring to this  link http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
> At 2015-05-11 08:39:39, Ming Tang <m21.tang at qut.edu.au> wrote:
>> Dear all,
>> I want to simulate a protein containing hydroxylysine (HYL). I checked all the force fields, but no .rtp file includes the parameters of it. How can I derive it correctly?
>> Thanks.
>> --
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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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