[gmx-users] pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 17:22:33 CEST 2014

On 6/18/14, 11:18 AM, mirko busato wrote:
> 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?

If you have non-amino acids as the termini (i.e. capping groups), you need to 
select "None" for both termini.  The side chain protonation is irrelevant to the 
treatment of the actual termini.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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