[gmx-users] Response required
Smith, Micholas D.
smithmd at ornl.gov
Sat Dec 29 15:01:19 CET 2018
Your using more atoms than LigParGen allows. Try generating a topology for a trimer, tetramer, and pentamer (if you can) and then use the resulting output topologies as a template for building 3 types of PEO residues: 1 with a linkage to the beginning of the chain, 1 with a linkage to the end of the chain, and one between two central monomers, in the gromacs rtp file.
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 molashahimaryam at aut.ac.ir <molashahimaryam at aut.ac.ir>
Sent: Friday, December 28, 2018 9:50:05 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Response required
When I submit a PEO chain consists of 23 monomers to LigParGen
web-based service to make a topology file, there is no problem. But when I submit a PEO chain consists of 100 monomers I give an error:
* Found residue ligand OXY
* Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code.
* How should I do?
This email was Anti Virus checked by Security Gateway.
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-request at gromacs.org.
More information about the gromacs.org_gmx-users