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<p class=MsoNormal style='text-indent:36.0pt'><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial'>Hi <span
style='mso-spacerun:yes'> </span>Anton !!!!!!!!! <o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><font size=2 face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial'>It´s</span></font></span><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>
the protein docked with its cofactor and coenzyme. There are two active sites
with one cofactor and one coenzyme in each one. I have already checked the
structure in <span class=SpellE>ProChek</span> and everything is OK. I have also
performed one round of steep descent EM until <span class=SpellE>emtol</span> =
1000 and further 1000 steps of cg. <span style='mso-spacerun:yes'> </span>I
suspect that the problem is really the molecules docked to the actives sites
cause without then the dynamics went well. I am looking now for any mistakes committed
in the <span class=SpellE>parametrization</span> and docking process.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span>There
is another detail in my job. I had to add 12 atoms of Na+ to neutralize the system.
Could this create any <span class=GramE>problem ?</span> <span
style='mso-spacerun:yes'> </span>If so, is it acceptable to run the job without
neutralize the <span class=GramE>system ???????</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span>Thanks
a lot for you <span class=GramE>help !!!!!!!!!!!!!!!!</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span>Best<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'><span
style='mso-tab-count:1'> </span><span class=SpellE>Tanos</span> C.
C. Franca.</span></font><font size=2 face="Courier New"><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>Christoph</span></font></span><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'> <span class=SpellE>Freudenberger</span>
wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> <span class=SpellE>Tanos</span>
C. C. <span class=SpellE>França</span> wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>>><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>>><span
style='mso-spacerun:yes'> </span>I am facing the problem of
segmentation fault again<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>>> !!!!!!!!!!!! This time I am
trying to perform a Position Restrained <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>>> (PR) molecular dynamics (MD)
of a crystallographic structure I have <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>[...]<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> You're using<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> <span class=GramE>constraints</span><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>all-bonds<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> <span class=GramE>with</span>
the default LINCS algorithm. Looks like your system gives coupled <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> <span class=GramE>constraints</span>
that cannot be resolved by LINCS (check the manual about <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>> that).<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>If it's just a protein, all-bonds
& <span class=SpellE>Lincs</span> should work.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Perhaps there are strange things in
your crystal structure.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Did you do EM before the MD? (You
*must*!)<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>Have you checked the crystal
structure with for example <span class=SpellE>ProCheck</span>?<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><span style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
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