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<DIV><SPAN class=898493117-02032006>I've searched through your database and
found many helpful suggestions, but I am not sure why mdrun successfully
runs on some files but not others.<SPAN class=983543712-03032006> The
protein files are pretty but I get the following results when running
mdrun. (Yesterday I tried attaching the files but they made the email too
big and it got returned)</SPAN></SPAN></DIV>
<DIV><SPAN class=898493117-02032006></SPAN> </DIV>
<DIV><SPAN class=898493117-02032006>ABPa1OUT.pdb fails (Number of grid cells is
zero. Probably the system and box collapsed.)</SPAN></DIV>
<DIV><SPAN class=898493117-02032006>QBPq1OUT.pdb succeeds with errors (<SPAN
class=330124816-02032006>some bonds rotated more than 30
degrees</SPAN>)</SPAN></DIV>
<DIV><SPAN class=898493117-02032006>GBPg1OUT.pdb succeeds</SPAN></DIV>
<DIV><SPAN class=898493117-02032006></SPAN> </DIV>
<DIV><FONT size=+0><SPAN class=898493117-02032006>
<DIV><SPAN class=330124816-02032006></SPAN><SPAN class=330124816-02032006><SPAN
class=898493117-02032006><FONT size=2>Also, the topology files for ABP and
GBP are made using 1 file, while the QBP topology file is made using 2
files. (when 2 files are used, I edit the topol.top file to have the
posre_A.itp and posre_B.itp files -- #include
"posre_A.itp")</FONT></SPAN></SPAN></DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
size=2></FONT></SPAN></SPAN> </DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
size=2>Here are the commands I'm running:</FONT></SPAN></SPAN></DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
face="Courier New" color=#800000 size=2>pdb2gmx -f file_name.pdb -o -p <
input.txt</FONT><FONT face="Courier New" size=2><BR></FONT><FONT
face="Courier New" color=#800000 size=2>editconf -bt octahedron -f -o -c -d
0.7</FONT><FONT face="Courier New" size=2><BR></FONT><FONT face="Courier New"
color=#800000 size=2>genbox -cp conf.gro -cs -o -p</FONT><FONT
face="Courier New" size=2><BR></FONT><FONT face="Courier New" color=#800000
size=2>grompp -f -c out.gro -p -o</FONT><FONT face="Courier New"
size=2><BR></FONT><FONT face="Courier New" color=#800000 size=2>mdrun -s -o -c
-g -e</FONT></SPAN></SPAN></DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
face="Courier New" color=#800000 size=2></FONT></SPAN></SPAN> </DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
face=Arial size=2>Thank you,</FONT></SPAN></SPAN></DIV>
<DIV><SPAN class=330124816-02032006><SPAN class=898493117-02032006><FONT
face=Arial size=2>Jennifer</FONT></SPAN></SPAN></DIV><FONT face="Courier New"
size=2></DIV></FONT></SPAN></SPAN></SPAN></FONT></DIV></FONT></DIV></BODY></HTML>