[gmx-users] rtp file
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 29 21:29:28 CET 2007
Quoting özge kül <ozgekul8233 at yahoo.com>:
> 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
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.
> Thank you very much
> Özge Kül
> Hacettepe University
> Chemistry Department
> "Justin A. Lemkul" <jalemkul at vt.edu> 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
> > 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
> > fatal error.
> You should not make changes to the .rtp file unless you absolutely know what
> you're doing.
> > 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
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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