[gmx-users] Re: multiple protein in a simulation box

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I may 
have written a tutorial, but that does not mean I am a private help service (as 
I have stated numerous times across the list).  Your question is not directly 
related to the content of the tutorial.

Comments below.

mohammad ghahramanpour wrote:
> Hi,
>  
> I read your tutorial about membrane protein simulation, it 
> was interesting,thanks for it.
>  
> I want to insert 2 copies of the peptide in a simulation box containing 
> 128 DPPC lipid molecules.
> For insertion the first copy I used below procedure:
>  
> VMD  dppc128.pdb
> File....
>     New Molecule....
>                         Peptide.pdb....
>                                          Laod....
> The peptide inseted in the interested location
> Save the new coordination of the peptide.....peptide_new.pdb 
> The crystline of the peptide_new.pdb is replaced bye the crystline of 
> the dppc128.pdb
> Then I used the genbox command:
>  
> genbox  -cp peptide_new.pdb  -cs dppc128.pdb  -o peptide_dppc.pdb
>  
> But when I used the same procedure for insertion the second copy of the 
> peptide, Gromacs shows seggmentation fault.
>  
> VMD  peptide_dppc.pdb
> File....
>     New Molecule....
>                         Peptide.pdb....
>                                          Laod....
> The second copy of the peptide inseted in the interested location
> Save the new coordination of the peptide.....peptide_second.pdb 
> The crystline of the peptide_second.pdb is replaced bye the crystline of 
> the peptide_dppc.pdb
> Then I used the genbox command:
>  
> genbox  -cp peptide_second.pdb  -cs peptide_dppc.pdb -o  
> 2copy_peptide_dppc.pdb...........seggmentation fault
>  
> Plesae guide me how can I Insert two copies of the peptide on the either 
> side of the membrane.
>  

If your goal is to simply place two peptides "above" and "below" the membrane, 
this is easily accomplished by positioning both peptides with editconf and 
solvating with genbox.  No need to invoke VMD or any other external program.

-Justin

> Thanks in adavnce
>  
> Mohammad Ghahremanpour

-- 
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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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