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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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