For any text file, use your favorite editor to delete all your water molecules. It will load very fast. For the xtc/trr files, use trjconv with an index file to write a new xtc/trr file without water molecules. Index file should contain the atom nos. of the molecules you want.<div>
<br></div><div>trjconv -s a.tpr -f a.xtc/trr -n a.ndx -o b.xtc/trr</div><div><br></div><div>chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Thu, Dec 8, 2011 at 10:56 AM, Saba Ferdous <span dir="ltr"><<a href="mailto:saba.bsbi154@iiu.edu.pk">saba.bsbi154@iiu.edu.pk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear Sir,<br>I need to ask you that if I want only pdb coordinates in the resultant md-noPBC.xtc/md-noPBC.pdb file rather than the solvant atoms and coordinates then what should I do. because the water box causes very delay in loading of frames and its difficult to viualize the trajectory. kindly help me to get out of the broblem. I only want that my protein get display in vmd rather than the water box.<br>
the size of md-noPBC.xtc is 612 Mb<br>md-noPBC.pdb is 13.2 GB<br><br>analysis is getting very slow and system is hanging. kindly help me out to fix this problem.<br><br>Regards <br>Thanks<span class="HOEnZb"><font color="#888888"><br>
<br clear="all"><br>-- <br>Saba Ferdous<div>
Research Scholar (M. Phil)</div><div>National Center for Bioinformatics</div><div>Quaid-e-Azam University, Islamabad</div><div>Pakistan</div><br>
</font></span><br>--<br>
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