[gmx-users] pdb2gmx

mirko busato busato.mirko at yahoo.com
Thu Jun 19 15:04:52 CEST 2014

Thank you very much for your quick reply,

My peptide is only composed of amino acids, and it has a total charge of 0.
My termini are NH2 and COOH (so the termini are not  ionized). My force field is amber99sb.
I tried to change  for all atoms of my first residue (ASN) the ASN residue with  the  NASN residue name. In the first residue (ASN) there are the 3 atoms of N terminal . In the same way for ARG (the last residue ) with CARG.

With -inter option  in the pdb2gmx command,
If I select Not protonated ARG (charge 0) and the other residues with charge 0, at the end the command says:
Fatal error
"In the chosen force field there is no residue type for 'ARGN' as an ending terminus"

if I select protonated ARG (charge 1) and the other residues  with charge 0, I obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and my COOH in COO. (The command works but in my case the result is wrong because the total charge has to be 0 with NH2 and COOH termini, not ionized).

I don't understand if in my case I have to change ASN to NASN only for the 3 atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C terminal ( C,O2,O1,H)

or change for all atoms of the first residue (ASN), ASN with NASN, and change all atoms of the last residue (ARG) , ARG with CARG.( that I done and described before)..
 If this is the right way, I don't know how to obtain the right result for my peptide.

Could you help me?

I attached  my original .pdb file (not edited), and my edited pdb file.

Thank you very much, 


On Wednesday, June 18, 2014 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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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