[gmx-users] protein-ligand complex mdrun errors

Vignesh Waran vigneshnivas09 at gmail.com
Fri Mar 17 17:44:02 CET 2017

respected sir,

  i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?

my command line   gmx mdrun -v -deffnm em

how to find the clarify the problem?
 pls tell me sir

GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em

*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*

Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this
machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*

bioinformatics at bioinformatics-desktop:~/Desktop/Gromacs$ ls
em.mdp     mdout.mdp      RET.pdb          RLBP_solv_ions.gro  topol.top
complex.gro  em.tpr     #mdout.mdp.1#  RLBP1.gro        solv.gro
drg.itp      ions.tpr   minim.mdp      RLBP1.pdb        #temp.topRLSaIL.1#
em.log       JZ4 model  posre.itp      RLBP_newbox.gro  #temp.topW9R5zG.1#

this file run the energy minimization

T. Vigneshnwaran,
M.Tech final year Bioinformatics,
Bharathidasan University,
Trichy, Tamilnadu, India.

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