[gmx-users] Re: Fatal error from mdrun, again
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. Kerrigans 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 dont understand why this error occurred.
I hope somebody can tell me how to fix it.
; Include forcefield parameters
[ molecules ]
; Compound #mols
; 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
Phone: 215-955-1364 (Lab)
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