Quoting özge kül <[EMAIL PROTECTED]>: > 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" <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > --------------------------------- > 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
