Re: [gmx-users] virtual site generation for backbone hydrogen

Sorry, I found the error. There was a bond -C N missing in the rtp file. Cheers, Jochen Am 12/17/12 5:28 PM, schrieb Jochen Hub: Hi all, I try to generate a topology using pdb2gmx of a protein that contains a non-native amino acid, that is "lysine with some more atoms", which is treated a one

[gmx-users] virtual site generation for backbone hydrogen

Hi all, I try to generate a topology using pdb2gmx of a protein that contains a non-native amino acid, that is "lysine with some more atoms", which is treated a one amino acid RETK. Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a constraint is generated between the bac