[gmx-users] add hydrogen atom in pdb file

Mark Abraham Mark.Abraham at anu.edu.au
Sun Dec 14 09:05:20 CET 2008

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.


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