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<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=322520819-26012004>make
sure you use the N-term pro option in pdbgmx and check atom types for N-term
patch in .top and .rtp (library file)</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=322520819-26012004>cheers</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=322520819-26012004>Marco</SPAN></FONT></DIV>
<BLOCKQUOTE dir=ltr
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> gmx-users-admin@gromacs.org
[mailto:gmx-users-admin@gromacs.org]<B>On Behalf Of </B>Huafeng
Xu<BR><B>Sent:</B> Monday, January 26, 2004 2:07 PM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> [gmx-users] terminal proline and
OPLSAA charges<BR><BR></FONT></DIV>
<DIV>
<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></BLOCKQUOTE></BODY></HTML>