Sounds like a bad VMD selection that didn't remove MNZ1 when you did the conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ in protonated LYS.
On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote: > Dear Gmx Users, > > I run implicit simulation for 1 us with virtual sites on hydrogens, then > using VMD extracted coordinates into the pdb file. As I want to run > explicit solvent simulation now I removed hydrogens so that pdb2gmx will > add them. Then I got an error while trying to pdb2gmx using Charmm27: > > Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms > while sorting atoms. > > How come this atom appears in my pdb file? Any suggestions? > > Thank you, > > Steven > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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