Dear Justin,
Thanks for the details. As you mentioned, I did not find any force field
which contains parameters for all metals.
Regards,
Shankar
On Fri, Dec 19, 2014 at 5:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/19/14 2:59 AM, Shankar Prasad Kanaujia wrote:
Dear users,
I had simulated one protein with metal Zn (Zinc) bound using Gromacs
version 4.5.5 with OPLSS-AA force field. Now, I am trying to rerun to
calculate the energy between two groups with Gromacs version 5.0.2. I am
getting the following error:
Atomtype ZN2+ not found.
Zn2+ and some other ions were removed from the OPLS-AA files because they
were not, in fact, actually OPLS-AA parameters. Note that this is stated
prominently in ffnonbonded.itp:
; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added
them.
Cu2+ Cu2+ 29 63.54600 2.000 A2.08470e-01
4.76976e+00
Fe2+ Fe2+ 26 55.84700 2.000 A2.59400e-01
5.43920e-02
Zn2+ Zn2+ 30 65.37000 2.000 A1.95200e-01
9.78219e-01
Ar Ar 18 39.94800 0.000 A3.41000e-01
2.74580e-02
I would rigorously evaluate whatever you did with 4.5.5 and consider
repeating the simulations with better parameters, if they exist, or using a
force field for which Zn2+ has been parametrized properly.
-Justin
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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Shankar Prasad Kanaujia, Ph.D.
Assistant Professor
Department of Biotechnology
Indian Institute of Technology Guwahati
Guwahati - 781039 Assam, India
Tele: 0361 258 2228
Fax: 0361 258 2249
Email: spkanau...@iitg.ernet.in
Homepage: http://www.iitg.ernet.in/spkanaujia/
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