[gmx-users] HYL force field

[Justin Lemkul]

On 5/11/15 8:19 AM, Ming Tang wrote:
>
> Dear Justin,
>
> The protein contains 15 constituent HYL residue modified from LYS. I realized that I need to modify the .rtp, but have no idea about how to derive the parameters correctly. Do you have any suggestions for this?
>

As I said, it depends on the force field you're using.  You need to look into 
the primary literature for the parent force field and derive the residue 
parameters in the same way to be compatible.

-Justin

> thanks a lot.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Monday, 11 May 2015 9:41 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] HYL force field
>
> 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.
>
> -Justin
>
>> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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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
http://mackerell.umaryland.edu/~jalemkul

==================================================