<div>Hi Justin A. Lemkul ,</div> <div> Thank you for your answer.Your answer made me clear suddenly.:)And I think I found the rigth way :) </div> <div> </div> <div>Thank you</div> <div>Özge Kül</div> <div><BR><BR><B><EM>"Justin A. Lemkul" <jalemkul@vt.edu></EM></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Quoting özge kül <OZGEKUL8233@YAHOO.COM>:<BR><BR>> Thank you Justin A. Lemkul for your interest of my question.I looked at my<BR>> 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with<BR>> that fatal error.I thougth that my pdb structure had wrong structure and then<BR>> I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an<BR>> idea?<BR><BR>The program ends in a fatal error because there is in fact no atom called LPD1<BR>within a methionine residue, as far as the force field (and most standard<BR>nomenclature) is
concerned. Read the error message: "atom LPD1 not found." If<BR>LPD1 is a lone pair, as you claim, than it is obviously not an atom, and hence<BR>why pdb2gmx is complaining. Is this residue something you modified in Sybyl? <BR>Because I can't find anything in 4htc.pdb that says LPD1.<BR><BR>-Justin<BR><BR>><BR>> Thank you very much<BR>> Özge Kül<BR>> Hacettepe University<BR>> Chemistry Department<BR>> "Justin A. Lemkul" <JALEMKUL@VT.EDU>wrote:<BR>> Quoting özge kül :<BR>><BR>> > Hi all,<BR>> ><BR>> > I try to use gromacs for my callculations of thrombin structure.I obtained<BR>> > the pdb from protein databank.But the structure has some missing residues<BR>> at<BR>> > the end of the chain and et the beginning of the chain.I completed the<BR>> > residues with sybyl 7.3.And then I started to my simulation.But in the<BR>> > pdb2gmx command I got this<BR>> ><BR>> > fatal error.:Atom LPD1 in MET11
not found in rtp entry with 9 atoms.<BR>><BR>> That means the residue has atoms that are named differently than those in the<BR>> .rtp file. If the atom does indeed belong, determine what it is and rename it<BR>> in the .pdb file, not the .rtp.<BR>><BR>> ><BR>> > Then I looked at the .rtp file.I want to learn how can I add a missing<BR>> > thing to the .rtp file.I search for the list that have the same titile.But<BR>> > one of you please write me how can I do this.My simulation is depend on<BR>> this<BR>> > fatal error.<BR>><BR>> You should not make changes to the .rtp file unless you absolutely know what<BR>> you're doing.<BR>><BR>> -Justin<BR>><BR>> ><BR>> > Thank you very much<BR>> > Özge Kül<BR>> ><BR>> > Hacettepe University<BR>> > Chemistry Department<BR>> ><BR>> ><BR>> > ---------------------------------<BR>> > Be a better sports nut! Let
your teams follow you with Yahoo Mobile. Try it<BR>> > now.<BR>><BR>><BR>><BR>> ========================================<BR>><BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>><BR>> ========================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>><BR>><BR>><BR>> ---------------------------------<BR>> Be
a better sports nut! Let your teams follow you with Yahoo Mobile. Try it<BR>> now.<BR><BR><BR><BR>========================================<BR><BR>Justin A. Lemkul<BR>Graduate Research Assistant<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul@vt.edu | (540) 231-9080<BR>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR><BR>========================================<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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