[gmx-users] pdb2gmx

mirko busato busato.mirko at yahoo.com
Wed Jun 18 17:18:12 CEST 2014

Dear Users,

I am using the command pdb2gmx_d on a neutral peptide in this way:

pdb2gmx_d -f pep2_n.pdb -water none -inter

My force field is AMBER. The first residue is ASN and the last residue is ARG
My terminals are not ionized (NH2 and COOH). So I changed the name of residue ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS in ACE for the  4 atoms (C,O2,O1,H2).

If in the interactive way I select ARG (not protonated) ,I obtained a message like that " Fatal error:
In the chosen force field there is no residue type for 'ARGN' ".

After I tried to select ARG(protonated) and I obtained this error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so    that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).

Could you help me?

Thank you very much,


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