[gmx-users] asking for N and C termini for DNA and giving error
csisd at nus.edu.sg
Tue Mar 18 04:27:52 CET 2014
Thanks Justin. I have very recently started doing MD, guided by Gromacs tutorials; not aware of this issue. Thanks for you suggestion, I will try with Amber ff.
Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: csisd at nus.edu.sg
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, March 17, 2014 7:49 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] asking for N and C termini for DNA and giving error
On 3/16/14, 11:35 PM, Sucharita Dey wrote:
> Thanks Justin.
> Since my protein has a modified DNA residue (methyl cytosine) I have copied the "gromos53a6.ff" folder as well as the "residuetypes.dat" file in my working directory and modified them, where I have inserted my modified DNA residue as DNA and also have renamed DADE, DTHY ... as DNA. Within "gromos53a6.ff", following "Adding a new residue" from gmx-tutorial, I have modified .rtp, .hdb, atomtypes.atp, and residuetypes.dat. In the rtp, hdb files as well DNA is written as DADE, DTHY.... And I am choosing this force field from the current directory while running pdb2gmx. It is not giving error for the modified residue but giving error for DNA terminal. Am I missing anything for which it is not identifying the DNA as "DNA"?
The Gromos96 53A6 force field does not have termini database entries for DNA or
RNA, so the nucleic acids are not fully functional. I don't know why you chose
this parameter set, but the nucleic acid parameters are far surpassed (in terms
of quality) by other force fields like AMBER and CHARMM. I would recommend you
use one of those, instead. They are also fully functional within Gromacs.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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