<html><body><P><FONT size=2 style="FONT-FAMILY: arial,helvetica,sans-serif">Hello gromacs users,</FONT></P>
<P><FONT size=2 style="FONT-FAMILY: arial,helvetica,sans-serif"> Greetings!</FONT></P>
<P><FONT size=2 style="FONT-FAMILY: arial,helvetica,sans-serif"> I am working with a docked complex. At present I am using GROMACS Dynamics simulation for my work. As a part of that I am using PRODRG server also for the inhibitor for which i need the gro coordinates and topology file. But when i submit the pdb coordinates of the same with hydrogens, it deletes the hydrogen from the inhibitor and gives the output. But I need the hydrogens to run the simulation.<BR><BR>The following is the output which i got:<BR><BR>========<BR>PRODRG> Starting up PRODRG version 050728.0532<BR>PRODRG> PRODRG written/copyrighted by Daan van Aalten<BR>PRODRG> <BR>PRODRG> Questions/comments to dava@davapc1.bioch.dundee.ac.uk<BR>PRODRG> <BR>PRODRG> When using this software in a publication, cite:<BR>PRODRG> A. W. Schuettelkopf and D. M. F. van Aalten (2004).<BR>PRODRG> PRODRG - a tool for high-throughput crystallography<BR>PRODRG> of protein-ligand complexes.<BR>PRODRG> Acta Crystallogr. D60, 1355--1363.<BR>PRODRG> <BR>PRODRG> <BR>PRODRG> PDB mode detected.<BR>PRODRG> WARNING: deleted hydrogen 1H1 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H1 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H2 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H2 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H6 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H6 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H7 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H7 from your input.<BR>PRODRG> WARNING: deleted hydrogen 3H7 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H8 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H8 from your input.<BR>PRODRG> WARNING: deleted hydrogen 3H8 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H9 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H9 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H10 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H10 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H12 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H12 from your input.<BR>PRODRG> WARNING: deleted hydrogen H13 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H14 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H14 from your input.<BR>PRODRG> WARNING: deleted hydrogen 3H14 from your input.<BR>PRODRG> WARNING: deleted hydrogen 1H18 from your input.<BR>PRODRG> WARNING: deleted hydrogen 2H18 from your input.<BR>PRODRG> WARNING: deleted hydrogen 3H18 from your input.<BR>PRODRG> Molecule complexity index: 2.00.<BR>PRODRG> WARNING: applied 1 unusual hybridisation fixup(s).<BR>PRODRG> 0 hydrogen(s) added.<BR>PRODRG> 19 bonds 7 ambiguous<BR>PRODRG> 26 bond angles 11 ambiguous<BR>PRODRG> 5 improper dihedrals 0 ambiguous<BR>PRODRG> 13 dihedrals 5 ambiguous<BR>PRODRG> 3 partial charges 0 ambiguous<BR>PRODRG> Net charge on molecule: 0.000<BR>PRODRG> Using charge groups.<BR>PRODRG> Writing GROMACS topology.<BR>PRODRG> GROMACS topology quality on 0-10 scale: 6.4<BR>PRODRG> Keeping old coordinates.<BR>PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.042<BR>PRODRG> RMSD from GROMOS angle ideality (degrees) : 4.151<BR>PRODRG> RMSD from GROMOS plane ideality (degrees) : 1.060<BR>PRODRG> Number of improper improper dihedrals : 0<BR>PRODRG> Writing: SCRHWMMPG<BR>PRODRG> Normal program end<BR>==================<BR><BR>please let me know, is there any option to add hydrogens in the gro and top file? Please let me know how to proceed with that.Without the hydrogens how will i study the interaction between enzyme and drug? If i run the energy minimisation without the hydrogens in the inhibitor is it correct? Which force field should i select? How to edit the files for my inhibitor to make the simulation work with the enzyme.Please help me out.<BR><BR> Looking forward to hear from u soon!<BR><BR> Thanking you!<BR><BR><BR><BR>"praise the lord!"<BR><BR><BR>With prayers,<BR>prettina</FONT> </P><br> <br><hr>I use Krify Mail - http://mail.krify.com Get yourmail at Krify today!<br></body></html>