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-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ??
Sent: Monday, 11 May 2015 11:03 AM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@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.t...@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
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University of Maryland, Baltimore
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