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<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> > </FONT></SPAN>Let me know how to make use of the
VMD to view the gromacs file of the drug-enzyme complex?<SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> </FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005>Start up VMD, click on "File", "New Molecule",
"Browse", find the molecule file (*.gro) and "Load"
it.</SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> > </FONT></SPAN>Is it possible to<SPAN
class=066233722-31052005><FONT face=Arial color=#0000ff>
</FONT></SPAN>visualize the same in the INSIGHT II before entering into
simulation or solvation step?<SPAN class=066233722-31052005><FONT face=Arial
color=#0000ff> </FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005>? Not sure what you are asking there. Depends on
what file formats you can load into Insight, if it can handle the *.gro file,
then you can load and view it.</SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> > </FONT></SPAN>What is the desired command to be
given to see the drug-enzyme complex with hydrogens added in gromacs?<SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> </FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005>Just load it up and all atoms present in the *.gro file
will be shown. Then change the representation to
suit.</SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff>> </FONT></SPAN>How to get the VMD software?<SPAN
class=066233722-31052005><FONT face=Arial
color=#0000ff> </FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT face=Arial color=#0000ff
size=2><SPAN class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT face=Arial color=#0000ff
size=2><SPAN class=066233722-31052005>Type "VMD" into google.com, or any other
search engine, find the VMD home page and get it from
there.</SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial color=#0000ff>></FONT></SPAN>Is
there any other molecular visualisation tool for viewing<SPAN
class=066233722-31052005><FONT face=Arial color=#0000ff>
</FONT></SPAN>the molecule?<SPAN class=066233722-31052005><FONT face=Arial
color=#0000ff> </FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005>There are plenty, few have been mentioned on this
emailing list, so try a search.</SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005></SPAN></FONT></FONT> </DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><FONT face=Arial color=#0000ff>Catch
ya,</FONT></SPAN></FONT></FONT></DIV>
<DIV><FONT face="Courier New, Courier, mono"><FONT size=2><SPAN
class=066233722-31052005><!-- Converted from text/plain format -->
<P><FONT size=2>Dr. Dallas Warren<BR>Lecturer<BR>Department of Pharmaceutical
Biology and Pharmacology<BR>Victorian College of Pharmacy, Monash
University<BR>381 Royal Parade, Parkville VIC
3010<BR>dallas.warren@vcp.monash.edu.au<BR>+61 3 9903
9073<BR>---------------------------------<BR>When the only tool you own is a
hammer, every problem begins to resemble a nail.</FONT>
</P></SPAN></FONT></FONT></DIV></BODY></HTML>