----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu> Date: Wednesday, June 2, 2010 6:18 Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms To: Gromacs Users' List <gmx-users@gromacs.org>
> > Nilesh Dhumal wrote: > >I have addes the "CO" residue. > >Coordinate file > > > >REMARK Accelrys Discovery Studio PDB file > >REMARK Created: Fri May 28 17:26:23 Eastern > Daylight Time 2010 > >HETATM 1 C1 > CO 0 - > 1.044 -0.027 0.066 0.00 > 0.00 C > >HETATM 2 O2 > CO 0 - > 0.009 0.642 -0.037 0.00 > 0.00 O > >HETATM 3 O3 > CO 0 - > 2.286 0.595 -0.030 0.00 > 0.00 O > >END > > > >in ffopla.rtp file. > > > >[ CO ] ; mandatory > >[ ATOMS ] ; mandatory > > C1 opls_974 1.00 1 > > O2 opls_975 -0.50 2 > > O3 opls_976 -0.50 2 > > > >[ bonds ] > > C1 O2 > > C1 O3 > > > >I have also addes new atoms typs in ffopls.atp file. > > > > These input files work fine for me. The error message > complained about an atom > named "O" so be sure you're using the input you think you > are. Something has > gotten confused somewhere. Perhaps the .pdb has column-formatting problems. Also, naming carbon dioxide "CO" and having two distinct atom types for its oxygen atoms, with non-neutral charge groups seems like asking for trouble... Mark > > -Justin > > >NIlesh > > > >On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote: > > > >>Nilesh Dhumal wrote: > >> > >>>Hello, > >>> > >>> > >>>I am getting the following error during pdb2gmx. > >>> > >>> > >>>Fatal error: Atom O in residue CO 1 not found in rtp entry > with 3 atoms > >>> while sorting atoms > >>> > >>>I checked the pdb file and ffopls.rtp file also. > >>> > >>> > >>And what did you find? To my knowledge there is no such > residue "CO" in > >>the ffoplsaa.rtp file. Is this something you've > added? Regardless, > >>there's a mismatch somewhere, so if you can't identify it, > post the text > >>of your coordinate file and the relevant .rtp entry to see if > someone else > >>can spot it. > >> > >>-Justin > >> > >> > >>>Nilesh > >>> > >>> > >>> > >>> > >>> > >>-- > >>======================================== > >> > >> > >>Justin A. Lemkul > >>Ph.D. Candidate > >>ICTAS Doctoral Scholar > >>MILES-IGERT Trainee > >>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://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read > >>http://www.gromacs.org/mailing_lists/users.php > >> > >> > >> > > > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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