This is a common error that has been discussed numerous times on this list (hint: check the archives). pdb2gmx is not magic, so also check out:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database With a name like MET, pdb2gmx is expecting methionine, not methane. -Justin Quoting Foh <[EMAIL PROTECTED]>: > Hello > > I ask to help. > Now I study program GROMACS. > Has taken for an example file PDB - the molecule of metane: > > ATOM 1 CT MET 1 3.875 0.678-8.417 1.00 0.00 > ATOM 2 HC MET 1 3.800 1.690-8.076 1.00 0.00 > ATOM 3 HC MET 1 4.907 0.410-8.516 1.00 0.00 > ATOM 4 HC MET 1 3.406 0.026-7.711 1.00 0.00 > ATOM 5 HC MET 1 3.389 0.583-9.366 1.00 0.00 > END > > Further I create files > methane.gro And methane.top > pdb2gmx-f methane.pdb-p methane.top-o methane.gro-missing > With use OPLS of potential (a position 3 in the program pdb2gmx) > 3) oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > > The message, that is deduced > fatal error - I can not find the description of the given atoms in base. > > Probably a mistake in the description of structure. > The image of the report I apply. > > I work with the version for Windows. > > I ask to help. ======================================== 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
