hello all,
i'm trying to find out the number of water molecules in the binding site of the protein across a 100ns trajectory file(.xtc).
i'm new to programing and simulations, I followed how to make a tcl script and i made one while sourcing this in vmd it is showing an error:"can not find channel named "outfile" ". Can someone help or suggestions or tools to find out the number of water molecules in each frame?
I'm attaching the script file i used.
The possible solution to this query to replace outfile with $outfile in last line.
still I am confused in this line "set a [atomselect top "(water within 3 of protein and oxygen)" frame $i]". is this a correct line or we should replace with "[atomselect top "name OW and same residue as within 3 of protein"]".
both are giving different results.
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