[gmx-users] New residue and vsite in pdb2gmx

Mahdi Tavakol mahditavakol at ymail.com
Fri Sep 2 07:47:58 CEST 2016

Dear Gromacs users
I added a new residue to Charmm36 potential using CGenFF. It works fine with pdb2gmx. However, when I use the option -vsite hydrogens, I got the following error:"Can't find dummy mass for type CG321 bonded to type CG321 in the virtual site database (.vsd files). Add it to the database!"Where should I add the dummy mass? In which section of .vdb file?
Any help is appreciated in advance.
Yours sincerelyMahdi Tavakol

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