[gmx-users] Simulation queries

[Acqualine Lobo]

Thanks!

I did try replacing HEM with HEME without shifting the columns. This time I
get an error for the missing H atoms and several warnings.

------------------------------------------------
WARNING: atom HA is missing in residue HEME 137 in the pdb file
         You might need to add atom HA to the hydrogen database of building
bloc
                                      k HEME
         in the file merged.hdb (see the manual)


WARNING: atom HB is missing in residue HEME 137 in the pdb file
         You might need to add atom HB to the hydrogen database of building
bloc
                                      k HEME
         in the file merged.hdb (see the manual)


WARNING: atom HC is missing in residue HEME 137 in the pdb file
         You might need to add atom HC to the hydrogen database of building
bloc
                                      k HEME
         in the file merged.hdb (see the manual)

etc etc..

Fatal error:
There were 30 missing atoms in molecule Other_chain_A2, if you want to use
this
                                       incomplete topology anyhow, use the
option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

------------------------------------------------

I did use the -ignh option with pdb2gmx, still I get this error!

Regards,
Acqualine Lobo
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