[gmx-users] Insertion of the protein into membrane with Gmembed

[Justin A. Lemkul]

James Starlight wrote:
> Dear Gromacs Users!
> 
> 
> 
> I have some questions about insertion protein into membrane with Gmembed
> 
> 1) I've used default parameters from gmembed manual for preparing input 
> for insertion
> 
> integrator     = md
> energygrp      = Protein
> freezegrps     = Protein
> freezedim      = Y Y Y
> energygrp_table
> energygrp excl = Protein Protein
> 
> Here Protein is my protein group in topology.top
> 
> 
> I've obtained 2 warning from gropp
> 
> WARNING 1 [file gmembed.mdp, line 27]:
>   Unknown left-hand 'energygrp' in parameter file
> 
> 
> 
> WARNING 2 [file gmembed.mdp, line 27]:
>   Unknown left-hand 'energygrp excl' in parameter file
> 
> What does it means ? If I ignore those warnings I've obtain
> 

Both of the warnings indicate typographical errors.  Please see the manual for 
proper keywords.

-Justin

> No energy groups defined. This is necessary for energy exclusion in the 
> freeze group
> 
> May be I should define freezegrps as my lipid group not a protein or use 
> ndx file as an alternative ?
> 
> Thanks,
> 
> James
> 

-- 
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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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