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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Nagasree Garapati <nagasree.garap...@mail.wvu.edu> Sent: Wednesday, March 07, 2018 8:25 AM To: gmx-us...@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) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.