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<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Dear
colleagues,<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>I
carried out successfully an MD simulation of a protein in water using the
GROMOS 96 force field with spce water.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>But I
have a problem in switching to OPLSaa.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>I
proceeded as usual:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>#
pdb2gmx -ff oplsaa -f pn.pdb -o pn2.pdb -p pn.top -his -ss </span></font><font
face="Times New Roman"><span lang=EN-US style='font-family:"Times New Roman"'>–</span></font><font
face=±¼¸²><span lang=EN-US style='font-family:±¼¸²'>water tip4p<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>#
editconf -bt octahedron -f pn2.pdb -o pn3.pdb -c -d 1.0<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>#
genbox -cp pn3.pdb -cs tip4p.gro -o pn_em.pdb -p pn.top<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>#
grompp -f em.mdp -c pn_em.pdb -p pn.top -o pn_em.tpr<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>At this
stage, I received an error message:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>===============================================================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>checking
input for internal consistency...<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>calling
/usr/bin/cpp...<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>processing
topology...<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Generated
332520 of the 332520 non-bonded parameter combinations<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Generating
1-4 interactions: fudge = 0.5<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Generated
332520 of the 332520 1-4 parameter combinations<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Excluding
3 bonded neighbours for Protein 1<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Excluding
2 bonded neighbours for SOL 36<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Excluding
2 bonded neighbours for SOL 4710<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>NOTE:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>
System has non-zero total charge: -5.000000e+00<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>processing
coordinates...<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>-------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Program
grompp, VERSION 3.3.1<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Source
code file: grompp.c, line: 448<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Fatal
error:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>number
of coordinates in coordinate file (pn_em.pdb, 20758)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>
does not match topology (pn.top, 20614)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>-------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>===============================================================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>So I
checked the pn_em.pdb and found that 4782 water molecules were added. However,
at the end of pn.top it says:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=FR style='font-size:10.0pt;font-family:±¼¸²'>====================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=FR style='font-size:10.0pt;font-family:±¼¸²'> [
molecules ]<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=FR style='font-size:10.0pt;font-family:±¼¸²'>;
Compound #mols<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=FR style='font-size:10.0pt;font-family:±¼¸²'>Protein
1<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=FR style='font-size:10.0pt;font-family:±¼¸²'>SOL
36<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>SOL
4710<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>====================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>I do
not understand why there are two classes of solvents.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Anyway,
I changed the number of SOL in pn.top to 4782 and run grompp again. But this
time I get the following warning:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>=================================================================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>processing
coordinates...<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Warning:
atom names in pn.top and pn_em.pdb don't match (MW - HW3)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>(more
than 20 non-matching atom names)<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>WARNING
1 [file "pn.top", line 15315]:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'> 36
non-matching atom names<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>
atom names from pn.top will be used<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'> atom
names from pn_em.pdb will be ignored<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>=================================================================<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Everything
was OK with GROMOS 96 and spce water.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Any
suggestions would be greatly appreciated.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;word-break:keep-all'><font
size=2 face=±¼¸²><span style='font-size:10.0pt;font-family:±¼¸²'>Sanghwa Han<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=±¼¸²><span lang=EN-US style='font-size:10.0pt;
font-family:±¼¸²'><o:p> </o:p></span></font></p>
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