[gmx-users] symtab get_symtab_handle error

Justin Lemkul jalemkul at vt.edu
Thu Nov 19 22:57:48 CET 2015

On 11/19/15 12:05 PM, Zhaleh Ghaemi wrote:
> Dear all,
> I'm running Gromacs 5.0 on a protein-RNA system. The simulations need to be
> extended. I used the replacement of the tpbconv in version 5.0, namely "gmx
> convert-tpr" to extend the simulations with the command:
> mx convert-tpr -s md.tpr -f md.cpt -extend 20000 -o md2.tpr
> the md2.tpr file was generated with no errors, however the  mdrun crashed
> generating this error:
> *Fatal error:symtab get_symtab_handle 799 not found*
> So my questions are, why this error is happening? and what is the correct
> way with which the simulations can be extended (or restarted in the case of
> crashed simulations) with Gromacs 5.0?

Do not supply a .cpt file to convert-tpr.  If a correctly generated .tpr file 
still generates an error, trying upgrading to the latest version (5.1.1) and try 



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


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