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<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-tab-count:1'> </span>Dear
Sergio,<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-tab-count:1'> </span>I
have faced recently this problem and I think I solved it simply by choosing the
option “0” (<span class=SpellE>gromacs</span> <span class=SpellE>forcefield</span>)
when running pdb2gmx. I am afraid this kind of problem happens because PRODRG runs
with GROMOS 87 and do not recognize GROMOS 96.<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-tab-count:1'> </span>Best
regards.<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-tab-count:1'> </span><span
class=SpellE>Tanos</span> C. C. Franca<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-tab-count:1'> </span></span></font><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>IME – Rio de Janeiro
- Brasil <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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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'>Message: 4<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'>Date: Mon, 07 Apr 2003 17:00:52 +0200<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'>To: gmx-users@gromacs.org<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'>From: Sergio <span class=SpellE>Manzetti</span>
<<span class=SpellE>sergio.manzetti@bio.uio.no</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'>Subject: [<span class=SpellE>gmx</span>-users]
NADP inferno<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'>Reply-To: gmx-users@gromacs.org<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'>Hi all, in regard with NADP in
simulation with this protein I have, after <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>taking</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>Daan's</span> and
<span class=SpellE>Davids</span> advices into account decided to generate the
PDB <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>of</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'> it through PRODREG, then simulate it
in vacuum, then in water and then <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>with</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'> the protein.<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'>The first <span class=SpellE>errror</span>
in this path is when using PDB2GMX (I use the PDB with <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'>polar</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>hydrogens</span>
only) :<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'>Fatal error: Atom NBO in residue NADP
1 not found in <span class=SpellE>rtp</span> database<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><span class=GramE>while</span>
sorting atoms<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'><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>The atomic nomenclature from <span
class=SpellE>Prodreg</span> is incorrect<span class=GramE>! ..using</span> <span
class=SpellE>Gromos</span> ore <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 style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>Gromacs</span></font></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'> force <span class=SpellE>field</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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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 style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>Stuck</span></font></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;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 style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>Sergio<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'><o:p> </o:p></span></font></p>
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