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<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Hi friends,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>I have compiled Gromacs
on native windows. The first two program in demo script (perl implementation of
script “demo”) work fine but genbox displays following output <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Reading solute
configuration<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Glycine aRginine
prOline Methionine Alanine Cystine Serine<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Containing 145 atoms in
13 residues<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Initialising van der
waals distances...<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Reading solvent
configuration<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.
1984"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>solvent configuration
contains 648 atoms in 216 residues<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Initialising van der
waals distances...<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Will generate new
solvent configuration of 2x2x2 boxes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Generating
configuration<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Sorting configuration<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Found 1 molecule type:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'> SOL
( 3 atoms): 1728 residues<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Calculating Overlap...<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>box_margin = 0.315<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Removed 2895 atoms that
were outside the box<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Succesfully made
neighbourlist<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>nri = 11448, nrj =
456822<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Checking
Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Checking
Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Added 488 molecules<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Generated solvent
containing 1464 atoms in 488 residues<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Writing generated
configuration to cpeptide_b4em.gro<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Glycine aRginine
prOline Methionine Alanine Cystine Serine<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Output configuration
contains 1609 atoms in 501 residues<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Volume
: 17.1176 (nm^3)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Density
: 1002.99 (g/l)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Number of SOL
molecules: 488<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Processing topology<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Back Off! I just backed
up cpeptide.top to ./#cpeptide.top.1#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><b><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black;font-weight:bold'>Cpeptide.top
file is of zero bytes now… and all further programs in the test fail
after this.<o:p></o:p></span></font></b></p>
<p class=MsoNormal><b><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black;font-weight:bold'><o:p> </o:p></span></font></b></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>Has anybody faced such
problem before? What is remedy for this problem?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'>With warm regards,<o:p></o:p></span></font></p>
<p class=MsoNormal><b><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black;font-weight:bold'>KEDAR<o:p></o:p></span></font></b></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:black'><o:p> </o:p></span></font></p>
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