Hi Justin, Thanx for your suggestion. But, I am not getting how to do correction in those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my simulation. I am not getting what is happening in the simulation...:(...:( kindly suggest.
With Thanx, Vivek 2008/8/13 Justin A. Lemkul <[EMAIL PROTECTED]> > There are two potential solutions to this error. For background, refer to: > > > http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > So your options are: > > 1. If the ligand is present in the .rtp file, make sure your atom > nomenclature corresponds to that of the force field. > 2. Remove the ligand and deal with its topology separately (search Google > for John Kerrigan's tutorial for enzyme-ligand systems). > > -Justin > > vivek sharma wrote: > >> Hi Nahren, >> Thanx for your help, I opened the pdb file with swisspdb viewer and then >> tried the pdb2gmx command over that pdb file and got the following error. >> >> Total mass 28295.072 a.m.u. >> Total charge 1.000 e >> Writing topology >> Processing chain 5 'E' (372 atoms, 9 residues) >> There are 0 donors and 0 acceptors >> There are 0 hydrogen bonds >> Warning: 'NDP' not found in residue topology database, trying to use >> 'NDPH' >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: pdb2gmx.c, line: 421 >> >> Fatal error: >> Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms >> while sorting atoms >> ------------------------------------------------------- >> >> and the error for the all atom forcefield were as follow. >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: resall.c, line: 436 >> >> Fatal error: >> Residue 'NDP' not found in residue topology database >> >> ------------------------------------------------------- >> >> any advice for this will be of great help for me. >> >> Thanx, >> Vivek >> >> 2008/8/12 nahren manuel <[EMAIL PROTECTED] <mailto: >> [EMAIL PROTECTED]>> >> >> Dear Vivek, >> you just have to download swisspdb and open your pdb file. Thats all >> you got to do and It is more than enough. If you have more than 2/3 >> residues missing then, make sure the Ramachandran plots are fine. >> Also try a simple minimization before begining gromacs. >> nahren >> >> --- On *Tue, 8/12/08, vivek sharma /<[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>>/* wrote: >> >> From: vivek sharma <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> >> Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found >> in residue PHE270 while adding hydrogens >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> Date: Tuesday, August 12, 2008, 6:34 PM >> >> >> Hi David, >> Thanx a lot again. can you please tell me the criteria or the >> standards to do such correction or can you suggest some link or >> tutorial for the same? >> whether swiss pdb can help in such cases? >> >> With Thanx, >> Vivek >> >> >> >> 2008/8/12 David van der Spoel <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> >> >> vivek sharma wrote: >> >> Hi There, >> >> I am new to molecular dynamics and GROMACS. >> While trying MD for 1XU9.pdb (pdbid) in the very 1st >> step on using the command.... >> >> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp >> -vsite hydrogen -water spce >> >> I got the following in the last of error..... >> ...... >> ...... >> ...... >> ....... >> N-terminus: NH3+ >> C-terminus: COO- >> WARNING: atom CE2 not found in residue 270 while adding >> atom >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: genhydro.c, line: 304 >> >> Fatal error: >> Atom CE2 not found in residue PHE270 while adding hydrogens >> ------------------------------------------------------- >> I tried the same with different force field and water >> models, but getting the same error again and again. >> any suggestion will be highly appreciated. >> >> >> You have an incorrect pdb file. An atom is missing. You have >> to fix it yourself. >> >> >> >> With thanx, >> Vivek >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org <mailto: >> gmx-users@gromacs.org> >> 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] <mailto: >> [EMAIL PROTECTED]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 >
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