[gmx-users] Not have PDB file of peptide

[Justin A. Lemkul]

swati shah wrote:
> Hello Gromacs Users,
> 
> If I don't have PDB file of any peptide then how  can I start the 
> simulation in Gromacs? Does Gromacs has any other way to convert peptide 
> into Gromacs file(.gro file) ? 

Strictly speaking, a .gro file is not required; almost any coordinate file 
format will do:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file

If you don't have any coordinate file whatsoever of your peptide, then you'll 
have to construct it:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

-Justin

> Please help me out.
> 
> -Swati
> 
> 

-- 
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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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