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Dear Sergio,
<p>If you look at FAQ´s at the PRODRG web, you will find:
<p>Q: Why does PRODRG insist on renaming my atoms? This is a major pain
when I'm sumitting my structure to the PDB!
<p> A: Most refinement programs require unique
atom identifiers (names). PRODRG therefore checks for duplicate atoms names
in your input, and if it finds them all
<br> atoms are renamed. You can prevent this by
using a simple trick. Consider ...
<p>Maybe you can find some help there!
<p>I´ve recently solved the same problem for a small ligand topology
for GROMOS96. I´ve used the GROMOS87 topology generated by PRODRG
(I think it works better if your input is a plain text picture) and converted
to GROMOS96 by hand comparing the parameters in the ifp file for G87 and
G96. Then you have to check wether all bond, angle, dihedral parameters
are OK. I saw some little problems with the chirality, some dihedrals,
angles... This is really tedious, but you can get it!
<br>Hope this help!
<br>with best wishes,
<br>Ruben
<br>
<p>"Tanos C. C. França" wrote:
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<div class=Section1>
<div class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><font face="Courier New"><font size=-1>Dear
Sergio,</font></font><o:p></o:p></span></div>
<div class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><font face="Courier New"><font size=-1>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.</font></font><o:p></o:p></span></div>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><font face="Courier New"><font size=-1>Best
regards.</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><font face="Courier New"><font size=-1>Tanos</span>
C. C. Franca</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>IME
- Rio de Janeiro - Brasil </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Message:
4</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Date:
Mon, 07 Apr 2003 17:00:52 +0200</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>To:
gmx-users@gromacs.org</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>From:
Sergio <span class=SpellE>Manzetti</span> <<span class=SpellE>sergio.manzetti@bio.uio.no</span>></font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Subject:
[<span class=SpellE>gmx</span>-users] NADP inferno</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Reply-To:
gmx-users@gromacs.org</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Hi
all, in regard with NADP in simulation with this protein I have, after </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=GramE><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>taking</span></span><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 </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=GramE><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>of</span></span><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 </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=GramE><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>with</span></span><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'>
the protein.</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>The
first <span class=SpellE>errror</span> in this path is when using
PDB2GMX (I use the PDB with </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=GramE><span lang=EN-US style='font-size:
10.0pt;font-family:"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>polar</span></span><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><span class=SpellE>hydrogens</span>
only) :</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Fatal
error: Atom NBO in residue NADP 1 not found in <span class=SpellE>rtp</span>
database</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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><font face="Courier New"><font size=-1>while</span>
sorting atoms</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span lang=EN-US style='font-size:10.0pt;font-family:
"Courier New";mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>The
atomic nomenclature from <span
class=SpellE>Prodreg</span> is incorrect<span class=GramE>!
..using</span><span
class=SpellE>Gromos</span> ore </font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=SpellE><span style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Gromacs</span></span><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</font></font></span><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span
class=SpellE><span style='font-size:10.0pt;
font-family:"Courier New";mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Stuck</span></span><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'>!</font></font><o:p></o:p></span>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><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>
<p class="MsoNormal" style="mso-layout-grid-align:none;text-autospace:none"><span style='font-size:10.0pt;font-family:"Courier New";
mso-ansi-language:PT-BR;mso-fareast-language:PT-BR'><font face="Courier New"><font size=-1>Sergio</font></font><o:p></o:p></span>
<p class="MsoNormal"><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p></o:p></span></div>
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<pre>--
___________________________________________
Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144, 28006 MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18</pre>
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