[gmx-users] Cytochrom C
d.mohammadyani at gmail.com
Tue Jan 17 16:50:45 CET 2012
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
Cytochrome C is a difficult protein to simulate :(
On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Dariush Mohammadyani wrote:
>> According your help and "pdb2gmx -his -missing" I could create input
>> files. Also I used grompp without error. However, for mdrun I got this
> Using the -missing flag is very dangerous. If you're using it to override
> warnings or errors that pdb2gmx is giving, your simulations will almost
> certainly be junk because the topology is broken.
> *Function type CMAP Dih. not implemented in ip_pert*
>> How can I figure it out?
> Without seeing your .mdp file and knowing which Gromacs version you're
> using, there's little anyone can do to help you. The error suggests you're
> trying to transform a CMAP dihedral using the free energy code, which
> cannot be done (per the error message).
> 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
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