[gmx-users] Extracting PDB files from .trr trajectory file

[Erik Lindahl]

Hi,

You probably selected "protein" as an output group. Either select  
"system" (i.e. everything), or use make_ndx to create a custom index  
file with your protein and heme.

Cheers,

Erik

On Monday, May 12, 2003, at 10:16 America/Los_Angeles, Mr.Sridhar wrote:

> I ran a MD simulation of  protein containing heme in water.
> I wanted to get pdb files of individual time steps. I gave the  
> following
> command.
> trjconv -f md_WT.xtc -o md_WT.pdb -sep
>
> The PDB files were generated buf without "heme" cofactor in it.
> How can we get files having both the protein + cofactor coordinates ?
>
> sridhar.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464