Im sorry for the confusion. I used an .itp file from the UCalgary site for dpc, I input a line
[ molecules ] ; molecule name nr. DPC 65 SOL 6305 in the dpc.top file. However, I generated the .gro file directly from the m65.pdb file from the UCalgary site using the editconf command. >> WARNING 1 [file dpc.top, line 28]: >> 18915 non-matching atom names >> atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65) >> atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb) On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> I used your tutorial but am getting the error message >> >> WARNING 1 [file dpc.top, line 28]: >> 18915 non-matching atom names >> atom names from dpc.top will be used >> atom names from dpc.gro will be ignore >> >> probably because my .top file was generated using a file generated thru >> PRODRG (only inputing 23 DPC molecules and then specifying 65 of those >> units) while the .gro file was created using the whole .pdb file of the >> micelle containing all 65 units. How can I fix this error? -maxwarn 1 >> doesn't seem to be doing the trick. >> > > I don't completely understand what you've done. PRODRG uses a single > molecule > to produce a topology that can then be #included in the system topology. > I > don't know how you inputted 23 molecules and then specified 65. What does > this > mean? > > Also note that PRODRG topologies are usually insufficiently accurate for > actual > use in simulations: > > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > > The source of the error could be one of several problems, please see: > > http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names > > -Justin > > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
