[gmx-users] Force field error
Smith, Micholas D.
smithmd at ornl.gov
Mon Mar 4 14:59:46 CET 2019
Hi Swapnil Bhujbal,
The parameters exist; however, the residue rtp file may not have entries for the phosphorylated residues. If you want to use pdb2gmx to you will need to add these residues into the rtp file associated with the force-field.
Hope that helps.
If you need to quickly perform the setup and do not want to mess around with the rtp file modifications, you may want to check out charmm-gui.org and use their input generator to get your topologies.
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 Swapnil Bhujbal <swapnilbhujbal18 at gmail.com>
Sent: Monday, March 4, 2019 8:12:37 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Force field error
I'm performing ligand-protein simulation. My protein has phosphothreonine
and phosphoserine residues. So I have cheched this forum and accordingly I
have downloaded Charm36 force field November 2018 (
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) and kept in my
installation directory (/usr/local/gromacs/share/gromacs/top). Upon hitting
pdb2gmx, I can see the downloaded force field for phosphorylated residues;
"Charm36" in the list, but after selecting this force field I got the
*Fatal error:Residue 'TPO' not found in residue topology database*
Please help me to solve this problem.
Thank you in advance.
Mr. Swapnil Bhujbal
School of Medicine,
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