Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro)
I used 13. GROMOS 53a6 force field "Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input." So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu) I get the following options. Which GLUTAMIC ACID type do you want for residue 1 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Both options give the same error as before. The same error occurs for HB1 as well. Will I have to edit the pdb or rtp file? Or any other suggestions? Thanks.. -- 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
