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<P><FONT face="Courier New, Courier, mono" size=2>Respected Sir,</FONT></P>
<P> Greetings in the name of the lord!</P>
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<P> <FONT face="Courier New, Courier, mono" size=2>I have taken a drug-enzyme complex in the form of the pdb file from the INSIGHT II software, without the hydrogens added. After transfering it to the Gromacs platform I have added up the hydogens by<BR>choosing the forecefield option 1(Gromacs force field with all hydrogens- proteins only). Let me know how to make use of the VMD to view the gromacs file of the drug-enzyme complex? Is it possible to<BR>visualize the same in the INSIGHT II before entering into simulation or solvation step? What is the desired command to be given to see the drug-enzyme complex with hydrogens added in gromacs? How to get the VMD software? Is there any other molecular visualisation tool for viewing<BR>the molecule? Please do mail me in detail about it. </FONT></P>
<P><FONT face="Courier New, Courier, mono" size=2> I just want to see if the residues around the active site are correctly protonated and also to see if the drug is in the right position in the enzyme as it was before transferring it to the Gromacs<BR>platform. Please do guide me. </FONT></P>
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<P><FONT face="Courier New, Courier, mono" size=2>Note: Please do let me know how to add hydrogens to the drug molecule, because i have edited the gro and top file of the enzyme with the drug .gro and .itp file which i obtained using the PRODRG server. I have tried visualizing the molecule with hydrogens , but the drug doesn't have the same. what to do? Please guide me. Let me know how to add hydrogens to the drug molecule. </FONT></P>
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<P><FONT face="Courier New, Courier, mono" size=2> Thanking you!</FONT></P>
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<P><FONT face="Courier New" size=2>With regards and prayers,</FONT></P>
<P><FONT face="Courier New" size=2>prettina</FONT></P><br> <br><hr>I use Krify Mail - http://mail.krify.com Get yourmail at Krify today!<br></body></html>