[gmx-users] how to generate a *.mdp file?

[Maria Sabaye Moghaddam]

Thanks a lot Anton.  For some reason *itp files 
 were not there.  I re-ran pdb2gmx, and now it 
 works.  


 Best, 
 Maria. 

 Quoting Anton Feenstra <feenstra at few.vu.nl>: 

 > Maria Sabaye Moghaddam wrote: 
 > 
 > > Hello; 
 > > 
 > >         I am very new with gromacs.  I am at the initial stages of
getting 
 > > a trihelix in water simulation going.  I have generated the *.gro and 
 > > *.top files, but I don't know how to generate an *.mdp file.  I
copied the 
 > 
 > > one from the "Getting Started" section, but I am getting error
messages 
 > > like: 
 > > filename_A.itp : No such file or directory 
 > > filename_B.itp : "  "    "     "  " 
 > 
 > This probably has nothing to do with your choice of mdp options. Your
.top 
 > file refers to (several) .itp file(s), which apparently cannot be
found. 
 > You mention that you generated your .top file, I assume that was using 
 > pdb2gmx. pdb2gmx should have generated the corresponding .itp files in 
 > addition to the .top file. Maybe you missed them when copying/moving
things 
 > to a different place? 
 > 
 > 
 > -- 
 > Groetjes, 
 > 
 > Anton 
 >   _____________