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On 15/10/2010 11:04 AM, Emanuel Birru wrote:
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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am about to calculate partition
coefficient of a water
molecule using gromacs 4.0.7 . To do the calculation I used
spc water model as
a solvent and as a solute, I just changed the solute’s residue
name and
use the same itp file as the spc.itp of gromacs with the name
sol.itp. I can
manage to put them in a box as a solute and solvent, but the
problem arise when
I start doing minimization. I tried to minimised using L-BFGS
and steep. The
error message that I got is the following<o:p></o:p></p>
<p class="MsoNormal">“Fatal error:<o:p></o:p></p>
<p class="MsoNormal">More than one settle type.<o:p></o:p></p>
<p class="MsoNormal">Suggestion: change the least use settle
constraints into 3
normal constraints.”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">You can get the minimization mdp (em1 and
em2) files and my solute
itp file (sol) at the following link.<o:p></o:p></p>
<p class="MsoNormal"><a moz-do-not-send="true"
href="http://hydra.pharm.monash.edu.au/md_project/em1.txt">http://hydra.pharm.monash.edu.au/md_project/em1.txt</a><o:p></o:p></p>
<p class="MsoNormal"><a moz-do-not-send="true"
href="http://hydra.pharm.monash.edu.au/md_project/em2.txt">http://hydra.pharm.monash.edu.au/md_project/em2.txt</a><o:p></o:p></p>
<p class="MsoNormal"><a moz-do-not-send="true"
href="http://hydra.pharm.monash.edu.au/md_project/sol.txt">http://hydra.pharm.monash.edu.au/md_project/sol.txt</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Could any one suggest a solution please.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Emanuel<o:p></o:p></p>
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<br>
Why do you need to change the residue name? If all you're doing is
changing a label, and that introduces a problem, then why introduce
a label? The atom indices should serve as a label.<br>
<br>
Mark<br>
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