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

Smith, Micholas D. smithmd at ornl.gov
Wed Mar 7 14:32:22 CET 2018

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.



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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