nafiseh farhadian wrote:
Dear Sir,
i'm one of the new gmx user. i have a problem with gromacs input file.
i'll be thanking if you help me.
i'm working on protein system. i have pdb and itp file. in itp file
there are hydrogen atoms but in pdb file no. so when i define top file
the number of atoms don't match to each other and i get a fattal error.
my forcefield in top file is ''ffgmx forcefield''. i'll be appriciate if
you help me.
Don't use ffgmx for new simulations... it's been deprecated for years,
and pdb2gmx points this out.
It's also always appropriate to cite the actual error message you
received, since if your interpretation of the problem was totally
reliable then you probably wouldn't need to be asking for help.
You might try the protonate utility, or using pdb2gmx on your structure
to generate your .top file.
Mark
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