[gmx-users] Geometry Optimization for Metal organic Frame works

[Smith, Micholas D.]

I would contact the OBGMX folks concerning this, as it sound like a software issue. If it works to produce a topology file for your initial coordinate system but not your optimized coordinates (presuming the same system composition, just modified geometry) than something seems amiss with their webserver.

Regards,

Micholas

===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nagasree Garapati <nagasree.garapati at mail.wvu.edu>
Sent: Wednesday, March 07, 2018 8:25 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Fw: Geometry Optimization for Metal organic Frame works

Thank You Micholas


I have created the topology files using initial input file in OBGMX and it shows that there are 20 unique bond terms, out of which there are 3 bonds between the metal ion and the N2 in linker.

However, when I tried to create topolgies using the optimized final output (final.gro) file in OBGMX, nothing is created I have empty files for both .top and .itp files.

I believe there is something wrong with the topology files, but I am not able to figure out where is the mistake.

Any suggestions ?


Thank You


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028<tel:304%20293-5028>(O)
304 276-3674(M)

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