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