[gmx-users] Fatal error from mdrun

[xiaobing tian]

Dear Groamcs users,


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.

 

Sincerely,

 

Xiaobing



Xiaobing Tian  Ph.D.
Department of Microbiology and Immunology
Thomas Jefferson University
1025 Walnut St., Suite 420
Philadelphia,  PA19107
Phone: 215-955-1364 (Lab)
Do you Yahoo!?
Yahoo! Mail - More reliable, more storage, less spam
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040320/d333a83f/attachment.html>