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<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT face=Tahoma
size=2></FONT></DIV><SPAN class=786050623-20012004><FONT face=Arial size=2>I am
trying to set up a topology file from a pdb file using pdb2gmx. My peptide
starts with a proline in the N-terminus. I ran the
command </FONT></SPAN></DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial size=2>pdb2gmx -f
ligand.pdb -o ligand -p ligand -i ligand</FONT></SPAN></DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial><FONT size=2>chose
OPLS-AA/L force field, and noticed that the total charge of the system, as
reported in the output of command, was 1.870e, NOT AN INTEGER. If I delete
the prolines from the N-terminus, the problem goes away. As long as the
peptide starts with a proline at the N-terminus, the total charge is not an
integer. What is going on? <SPAN class=774340119-26012004><FONT
color=#0000ff> </FONT></SPAN></FONT></FONT></SPAN></DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial size=2>I am attaching the
PDB file of the peptide for your reference.</FONT></SPAN></DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2>Thanks.</FONT></SPAN></DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=786050623-20012004><FONT face=Arial
size=2>Huafeng</FONT></SPAN></DIV></BODY></HTML>