Thankl you. Well... Indeed, just removed them manually and everything is ok.
Steven On Mon, Apr 16, 2012 at 2:38 PM, Peter C. Lai <p...@uab.edu> wrote: > 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 >
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