[gmx-users] Cytochrom C

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 17 16:54:56 CET 2012

Dariush Mohammadyani wrote:
> Dear Justin,
> You are right, I had some warning and with -missing I override them, e.g.:
> WARNING: atom HA is missing in residue HEM 105 in the pdb file
> WARNING: atom HB is missing in residue HEM 105 in the pdb file
> ...
> 30 missing atoms. I did not know how should figure them out. I am using 
> GROMACS 4.5.3
> and charmm27.ff.
> Cytochrome C is a difficult protein to simulate :(

You'll make your life more difficult by overriding error messages you don't 
understand ;)

If all of the missing atoms are hydrogens, then a suitable .hdb entry must be 
constructed for the heme group so that the H atoms are all rebuilt. 
Alternatively, you can add them with some external modeling software capable of 
such tasks.  If there are other missing atoms, they too need to be added.  You 
must begin with an intact model, or otherwise have the ability to produce one.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list