[gmx-users] pdb2gmx

[mirko busato]

Thank you very much,

In my analysis ,I would like to consider Hydrogen bonds involving S atom as well.  I think that g_hbond is not built to manage Hydrogen bonds with S.

Do you know if there are available scripts? or Could you suggest me something to solve this problem?

I really appreciate your help

Mirko



On Friday, June 20, 2014 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 6/20/14, 10:12 AM, mirko busato wrote:
> Thank you,
>
> I understood,  you are right, in the .rtp file  there are not neutral form for
> the termini.
>
> What can I do to have a neutral arginine, to have at least a total charge of 0?
>
> Because In my case I am forced to choose ARG protonated else I get the error.
>
> Fatal error
> "In the chosen force field there is no residue type for 'ARGN' as an ending
>   terminus"
>

Use a force field that has parameters for a neutral form.  I'm sure someone has 
produced parameters for such a species, but they're not included in Amber99SB by 
default.  If parameters are out there, add them 
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), otherwise 
use a different force field.

-Justin

> Thank you very much,
>
> Mirko
> On Thursday, June 19, 2014 3:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 6/19/14, 8:59 AM, mirko busato wrote:
>  > 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.
>  >
>
> Look at the force field .rtp file - you will see that the Amber termini are
> predefined and they are always charged.  That is an unfortunate limitation to
> the current implementation.  I suspect someone must have produced neutral forms
> of the termini, but you'll have to add them yourself if you want to do such a
> simulation with this force field.
>
>  > 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"
>  >
>
> This option chooses the side chain protonation state, not the 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.
>  >
>
> As stated above, you'll have to modify the force field to add appropriate
> parameters or otherwise use a different force field that actually allows you to
> choose terminus protonation state.
>
>
> -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
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul

>
> ==================================================
>
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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