[gmx-users] is there any reasonable way to produce a custom topology?

[Yegor Isakov]

I would be extremely pleased if anybody would tell me how could I foce that stupid pdb2gmx program to follow the path to the directory containing .itp files (~/share/top).
 Although in the manual it was recomended to avoid modifying .rtp files, that is the only way I found to produce a topology "semi-automatically." Is there any other  reasonable way to produce a topology? Is anywhere more intelegent converter of pdb files? Is anywhere a program that permits creating a stable bond between 2 atoms  in a topolgy without blowing up the last one? 
 
		
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