[gmx-users] rtp file

[özge kül]

Hi Justin A. Lemkul ,
   Thank you for your answer.Your answer made me clear suddenly.:)And I think I found the rigth way :) 
   
  Thank you
  Özge Kül
  

"Justin A. Lemkul" <jalemkul at vt.edu> wrote:
  Quoting özge kül :

> Thank you Justin A. Lemkul for your interest of my question.I looked at my
> 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with
> that fatal error.I thougth that my pdb structure had wrong structure and then
> I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an
> idea?

The program ends in a fatal error because there is in fact no atom called LPD1
within a methionine residue, as far as the force field (and most standard
nomenclature) is concerned. Read the error message: "atom LPD1 not found." If
LPD1 is a lone pair, as you claim, than it is obviously not an atom, and hence
why pdb2gmx is complaining. Is this residue something you modified in Sybyl? 
Because I can't find anything in 4htc.pdb that says LPD1.

-Justin

>
> Thank you very much
> Özge Kül
> Hacettepe University
> Chemistry Department
> "Justin A. Lemkul" wrote:
> Quoting özge kül :
>
> > Hi all,
> >
> > I try to use gromacs for my callculations of thrombin structure.I obtained
> > the pdb from protein databank.But the structure has some missing residues
> at
> > the end of the chain and et the beginning of the chain.I completed the
> > residues with sybyl 7.3.And then I started to my simulation.But in the
> > pdb2gmx command I got this
> >
> > fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms.
>
> That means the residue has atoms that are named differently than those in the
> .rtp file. If the atom does indeed belong, determine what it is and rename it
> in the .pdb file, not the .rtp.
>
> >
> > Then I looked at the .rtp file.I want to learn how can I add a missing
> > thing to the .rtp file.I search for the list that have the same titile.But
> > one of you please write me how can I do this.My simulation is depend on
> this
> > fatal error.
>
> You should not make changes to the .rtp file unless you absolutely know what
> you're doing.
>
> -Justin
>
> >
> > Thank you very much
> > Özge Kül
> >
> > Hacettepe University
> > Chemistry Department
> >
> >
> > ---------------------------------
> > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
> > now.
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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