[gmx-users] Re: Fatal error from mdrun, again

xiaobing tian xiaobingtian at yahoo.com
Mon Mar 22 15:40:01 CET 2004

Dear Groamcs users,

I have searched the archive and did not find similar questions. I have to send the question again.

I am currently using Gromacs tutorial from Dr. Kerrigan’s lab in Linux Red Hat 8.0. I selected Gromacs Force field. My system has a nonzero total charge(+2.0). Using genion command, I added two Cl to the system, and then corrected the fws.top. A line( #include “ions.itp”) was added and [molecules] section was also edited ( see below). The energy minimization was finished smoothly. At this point, I started position-restrained MD. After I modified the temperature coupling scheme for my pr.mdp file (see below), the grompp generated fws_pr.tpr file without any problems. But mdrun resulted in a fatal error: “Can not read/write topologies to file type unknown”. I don’t understand why this error occurred.

I hope somebody can tell me how to fix it.


; Include forcefield parameters

#include "ffgmx.itp"

#include “ions.itp”


[ molecules ]

; Compound        #mols

Protein             1

SOL               3125

Cl                  2


; Berendsen temperature coupling is on in three groups

Tcoupl              =  berendsen

tau_t               =  0.1          0.1   0.1

tc-grps             =  Protein      SOL   Cl

ref_t               =  300          300   300



I would really appreciated any help.





Xiaobing Tian  Ph.D.
Department of Microbiology and Immunology
Thomas Jefferson University
1025 Walnut St., Suite 420
Philadelphia,  PA19107
Phone: 215-955-1364 (Lab)
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