<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=ks_c_5601-1987">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:¹ÙÅÁ;
panose-1:2 3 6 0 0 1 1 1 1 1;}
@font-face
{font-family:±¼¸²;
panose-1:2 11 6 0 0 1 1 1 1 1;}
@font-face
{font-family:±¼¸²Ã¼;
panose-1:2 11 6 9 0 1 1 1 1 1;}
@font-face
{font-family:"\@±¼¸²";
panose-1:2 11 6 0 0 1 1 1 1 1;}
@font-face
{font-family:"\@±¼¸²Ã¼";
panose-1:2 11 6 9 0 1 1 1 1 1;}
@font-face
{font-family:"\@¹ÙÅÁ";
panose-1:2 3 6 0 0 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-autospace:none;
word-break:break-hangul;
font-size:10.0pt;
font-family:¹ÙÅÁ;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
{margin:0cm;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-autospace:none;
word-break:break-hangul;
font-size:10.0pt;
font-family:¹ÙÅÁ;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:±¼¸²;
color:windowtext;}
/* Page Definitions */
@page Section1
{size:595.3pt 841.9pt;
margin:99.25pt 3.0cm 3.0cm 3.0cm;
layout-grid:18.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=KO link=blue vlink=purple>
<div class=Section1 style='layout-grid:18.0pt'>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Dear gromacs users,<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><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 style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>I am running MD for a
protein with 212 amino acid residues.<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>When I run grompp (</span></font><font
face=±¼¸²Ã¼><span lang=EN-US style='font-family:±¼¸²Ã¼'>grompp -f pn_md.mdp -c
pn_md.pdb -r pn_md.pdb -p pn.top -o pn_md.tpr</span></font><font face=±¼¸²><span
lang=EN-US style='font-family:±¼¸²'> ) for the final product MD, I receive the
following error message.<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>I properly included sol and
ion in the temperature control part of pn_md.mdp.<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><i><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²;font-style:italic'>If I
include </span></font></i><i><font face=Arial><span lang=EN-US
style='font-family:Arial;font-style:italic'>¡°</span></font></i><i><font
face=±¼¸²><span lang=EN-US style='font-family:±¼¸²;font-style:italic'>define = </span></font></i><i><font
face=Arial><span lang=EN-US style='font-family:Arial;font-style:italic'>–</span></font></i><i><font
face=±¼¸²><span lang=EN-US style='font-family:±¼¸²;font-style:italic'>DPORRES</span></font></i><i><font
face=Arial><span lang=EN-US style='font-family:Arial;font-style:italic'>¡±</span></font></i><i><font
face=±¼¸²><span lang=EN-US style='font-family:±¼¸²;font-style:italic'> in
pn_md.mdp, both grompp and mdrun work fine.<o:p></o:p></span></font></i></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>The topolofy file pn.top
worked well in the previous steps (em.mdp and pr.mdp).<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Any suggestions would be
appreciated.<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><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 style='layout-grid-mode:char'><font size=2 face=±¼¸²><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²'>Sanghwa Han<o:p></o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²Ã¼><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²Ã¼'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='layout-grid-mode:char'><b><font size=2 face=±¼¸²Ã¼><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²Ã¼;font-weight:bold'>[Error
Message]<o:p></o:p></span></font></b></p>
<p class=MsoNormal style='layout-grid-mode:char'><font size=2 face=±¼¸²Ã¼><span
lang=EN-US style='font-size:10.0pt;font-family:±¼¸²Ã¼'>creating statusfile for 1
node...<br>
' for variable integrator, using 'md'<br>
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'<br>
' for variable ns-type, using 'Grid'<br>
Next time use one of: 'Grid' 'Simple'<br>
' for variable coulombtype, using 'Cut-off'<br>
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
'Reaction-Field-nec' 'Encad-shift' 'PME-User'<br>
' for variable optimize_fft, using 'no'<br>
Next time use one of: 'no' 'yes'<br>
' for variable tcoupl, using 'No'<br>
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'<br>
' for variable Pcoupl, using 'No'<br>
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'<br>
' for variable gen-vel, using 'no'<br>
Next time use one of: 'no' 'yes'<br>
' for variable constraints, using 'none'<br>
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#<br>
checking input for internal consistency...<br>
....ling /usr/bin/cpp <br>
: no such file or directory<br>
cpp: warning: '-x c' after last input file has no effect<br>
cpp: no input files<br>
cpp exit code: 256<br>
-I/usr/local/gromacs/share/gromacs/top pn.top > gromppcHKNXc'<br>
' command is defined in the .mdp file<br>
processing topology...<br>
processing coordinates...<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.1<br>
Source code file: grompp.c, line: 448<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file (pn_md.pdb, 34158)<br>
does
not match topology (pn.top, 0)<br>
-------------------------------------------------------</span></font><font
face=±¼¸²><span lang=EN-US style='font-family:±¼¸²'><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>
</div>
</body>
</html>