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,
Mirko
On Wednesday, June 18, 2014 5:20 PM, Justin Lemkul <jalem...@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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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