[gmx-users] regarding missing atom

[Justin A. Lemkul]

subramaniam boopathi wrote:
> dear sir,
>         i was doing gromacs when i run pdb2gmmx i got following error 
> that is some atom missing
> 

You need to provide an intact structure to pdb2gmx.  You will have to use other 
software to replace the missing atoms.  There are various programs that can do this.

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

-Justin

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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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