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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I was very excited to discover Gromacs and decided to learn
by following a few tutorials I found online. However, I ran into a problem:
After filling up the simulation box with SPC water using genbox, the program
backed up the topology file into another file with its name flanked by #, and
left me with an empty topology file. Without knowing what had happened I went
ahead and ran grompp, which exited with a fatal error, saying the number of
atoms in the topology file does not match that of the coordinate file. I tried
to use the backed up topology file, or to generate a new topology file using
pdb2gmx, but ended up with the same error message. Grompp thinks there is no
atom in the topology files.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Does anyone know what is going on? Also, water molecules don’t
seem to appear in topology files. Does that matter?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thank you very much if you have read this much. Any idea
what’s going on. Your help will be greatly appreciated.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Yun Li</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Assistant Professor of Chemistry</span></font><o:p></o:p></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Delaware</span></font></st1:PlaceName><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> <st1:PlaceType
w:st="on">Valley</st1:PlaceType> <st1:PlaceType w:st="on">College</st1:PlaceType></span></font></st1:place><o:p></o:p></p>
<p class=MsoNormal><st1:Street w:st="on"><st1:address w:st="on"><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>700 E. Butler
Ave.</span></font></st1:address></st1:Street><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>,</span></font><o:p></o:p></p>
<p class=MsoNormal><st1:place w:st="on"><st1:City w:st="on"><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Doylestown</span></font></st1:City><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>, <st1:State
w:st="on">PA</st1:State> <st1:PostalCode w:st="on">18901</st1:PostalCode></span></font></st1:place><o:p></o:p></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>(215) 489-2482</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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