Thank you Mark and Justin, your replies were very helpful . I was converting output file back into pdb file using "genconf" as I wanted to find out the structural changes happening(Ex: conformational changes ) after every operation. Is there any other way to tack progress of my task(Ex: Hydration ) .<br>
<br>Harshith<br><br><div class="gmail_quote">On Fri, May 30, 2008 at 2:26 AM, h a <<a href="mailto:y600100@gmail.com">y600100@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear users,<br><br>I am a beginner with gromacs. I converted a sample pdb file to gromacs file using "pdb2gmx" and then converted it back to pdb file using "genconf" but I found that positions of atoms was changed and so was their thermal factor. I did not understand why there was change in position of the atoms. when I observed both of them using pymol I found inconsistency in type of atoms and bond locations.<br>
<br>can you please explain why this happened .<br><br>thank you,<br><br>Harshith <br><br> <br>
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