[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

Hi everyone

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?

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