On 10/3/19 5:46 PM, Sarah Lucas wrote:
Dear GMX experts, I am trying to model a protein building its ligand but am having trouble generating the ions before I proceed with the energy minimization. I have been following the Protein-Ligand tutorial and able to make the commands run non-interactively using MPI. I tried following http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts to no avail. Currently, I am using Gromacs/2016.4.d with intel/2018.5.274 and impi same version. I tried using Gromacs/2019.1. My other option is version 5.0.4 Does anyone have a suggestion how to run genion non-interactively? Below are the line from my slurm file and the outputs it generated. SLURM file command: mpirun -np $MPI_NTASKS gmx_mpi_d genion -s wt_model_ions.tpr -o wt_model_solv.ions.gro -p topol_model.top -nname CL -nn 3 < sol.txt sol.txt contains 15 Error File: Fatal error: Group 0 ( System) has 105532 elements Group 1 ( Protein) has 6216 elements Group 2 ( Protein-H) has 3110 elements Group 3 ( C-alpha) has 399 elements Group 4 ( Backbone) has 1197 elements Group 5 ( MainChain) has 1595 elements Group 6 ( MainChain+Cb) has 1963 elements Group 7 ( MainChain+H) has 1966 elements Group 8 ( SideChain) has 4250 elements Group 9 ( SideChain-H) has 1515 elements Group 10 ( Prot-Masses) has 6216 elements Group 11 ( non-Protein) has 99316 elements Group 12 ( Other) has 49 elements Group 13 ( LIG) has 49 elements Group 14 ( Water) has 99267 elements Group 15 ( SOL) has 99267 elements Group 16 ( non-Water) has 6265 elements Select a group: ------------------------------------------------------- Program: gmx genion, version 2016.4 Source file: src/gromacs/topology/index.cpp (line 930) MPI rank: 3 (out of 16) Fatal error: Cannot read from input
MPI builds have problems reading from streams like this. No GROMACS tool benefits from MPI except mdrun, so use a non-MPI gmx binary for everything else.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
