[gmx-users] CG to FG transformation error

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi,
> 
> I have successfully converted my CG (only) protein model to FG model 
> using g_fg2cg command of the gromacs_reverse package. But now when I try 
> to compile my .mdp file for SA run, grompp is throwing some warnings:
> 
> creating statusfile for 1 node...
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> WARNING 1 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'cap_force' in parameter file
> 
> WARNING 2 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'cap_a' in parameter file
> 
> WARNING 3 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'fc_restr' in parameter file
> 
> WARNING 4 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'r_CGW' in parameter file
> 
> WARNING 5 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'fc_restrW' in parameter file
> 
> WARNING 6 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'rel_steps' in parameter file
> 
> WARNING 7 [file fg_protein.mdp, line unknown]:
>   Unknown left-hand 'rel_water' in parameter file
> 
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> ---------------------------------------------------------------------------------------------------------
> 
> My system contains only multiple copies of a protein. How to solve this 
> issue?
> Any suggestion is welcome.
> 

Use proper .mdp settings.  You're being told that your "fg_protein.mdp" contains 
numerous keywords that do not exist in normal Gromacs.

-Justin

> 
> Thanks,
> 
> -Anirban
> 

-- 
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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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