[gmx-users] protein-ligand complex mdrun errors

[Justin Lemkul]

On 3/17/17 12:43 PM, Vignesh Waran wrote:
> 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*
>

This suggests that you're linking against the wrong version of a library.  How 
did you install GROMACS (what was your exact cmake command)? And what does ldd 
tell you about the libraries to which mdrun is linked?

-Justin

>
> 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
>  #topol.top.1#
> drg.itp      ions.tpr   minim.mdp      RLBP1.pdb        #temp.topRLSaIL.1#
>  #topol.top.2#
> em.log       JZ4 model  posre.itp      RLBP_newbox.gro  #temp.topW9R5zG.1#
>
> this file run the energy minimization
>
>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================