[gmx-users] Cytochrom C

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 17 16:33:02 CET 2012

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 
> error:  

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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