<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><HTML DIR=ltr><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"></HEAD><BODY><DIV><FONT face='Arial' color=#000000 size=2>I am trying to run a simulated annaeling simulation on a 6
residue peptide which i chopped out of beta lactoglobulin.</FONT></DIV>
<DIV><FONT face=Arial size=2>I am using Windows and grommpp
absolutely refuses to work. I have read a previous posting that this error is
down to the path for the cpp not being set right in the mdp file. However no
matter how i change the path it results in this error</FONT></DIV>
<DIV><FONT face=Arial size=2>I think it might have to do with the fact that
theres a space in the path. however i cannot reinstall it as i do not have the
privileges on the network to do so. Is there a way round this kind of
situation</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanking you in advance</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Saif</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>grompp.mdp has this in it at the
moment</FONT></DIV>
<DIV><FONT size=2>
<P>title = Beta-Lac</P>
<P>cpp = c:\Progra~1\Gromacs\bin\cpp </P><FONT size=2>
<P>include = -I C:\Progra~1\Gromacs\share\top </P></FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>and running grompp results in</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>calling c:\Progra~1\Gromacs\bin\cpp...<BR>\Progra~1\Gromacs\bin\cpp:
Files\Gromacs\share\top: No such file or directory<BR>cpp exit code: 33<BR>Tried
to execute: 'c:\Progra~1\Gromacs\bin\cpp -I C:\Progra~1\Gromacs\share\top<BR>-I
D:\Gromacs\share\top -IC:\Program Files\Gromacs\share\top topol.top >
grompp<BR>a01720'<BR>The 'c:\Progra~1\Gromacs\bin\cpp' command is defined in the
.mdp file<BR>processing topology...<BR>processing coordinates...<BR>Fatal error:
number of coordinates in coordinate file (conf.gro,
23727)<BR>
does not match topology (topol.top, 0)</DIV></BODY></HTML>