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

Erik Lindahl lindahl at stanford.edu
Mon May 12 06:57:01 CEST 2003


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.



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.
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Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
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