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<DIV><FONT face=Arial size=2>does the pdb have CONNECT entries?</FONT></DIV>
<DIV><FONT face=Arial size=2>If the pdb has not this entries, when you read the
file with VMD for e.g., the program does a distance search, and then draws the
bonds between the atoms. If the structure is poorly defined, there's a great
possibility of having wrong bonds on your display.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>But, if you do a EM or small MD on the structure
....</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=absalomz2002@yahoo.com.mx
href="mailto:absalomz2002@yahoo.com.mx">Absalom Zamorano</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, March 18, 2005 7:24
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] Problems with a
PDB</DIV>
<DIV><BR></DIV>
<DIV>
<DIV>HI gromacs-friends...Firstly thank you for your help in previous
messages...Im starting in this forum and Its seems to me fantastic...</DIV>
<DIV>Now another question... I have a pdb file and contains all the atoms that
are theorically corrects. I mean the molecule is complete. But when I
visualize this file with VMD or VEGA, programs dont show all the bonds I
expect. </DIV>
<DIV>I will appreciate your commentaries..</DIV>
<DIV>Greetings...</DIV></DIV>
<P><BR>
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