<font color="#000099">This tutorial doesn't seem to be quite useful, if so many error</font><span style="color: rgb(0, 0, 153);">s pop up. Maybe it was implemented for Gromacs < 4.5.x but there's no info on the version it should be used.</span><br style="color: rgb(0, 0, 153);">
<br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x tutorials :D (<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a>) I'll give a try with the Lyzosyme one!</span><br style="color: rgb(0, 0, 153);">
<br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">- Jose</span><br style="color: rgb(0, 0, 153);"><br><div class="gmail_quote">On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
Jose Borreguero wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi Justin, thanks for your reply!<br>
<br>
I appended '-p protein.top' to genion. File protein.top was automatically updated by insertion of the following lines at the end of the file:<br></div>
/[ molecules ]<div class="im"><br>
; Compound #mols<br>
Protein_chain_A 1<br>
SOL 7791<br>
NA+ 26<br></div>
CL- 23/<div class="im"><br>
<br>
My solvated PDB, protein-solvent.pdb contains lines like these:<br>
ATOM 24543 NA NA+ 8043 50.712 66.452 12.341 1.00 0.00<br>
<br>
Now when I run grommp, I get the error<br></div>
/Fatal error:<br>
No such moleculetype NA+/<div class="im"><br>
<br>
I checked file gromos45a3.ff/ions.itp. The sodium is included in this fashion:<br></div>
/[ moleculetype ]<div class="im"><br>
; molname nrexcl<br>
NA 1<br>
[ atoms ]<br>
; id at type res nr residu name at name cg nr charge mass<br></div>
1 NA+ 1 NA NA 1 22.9898/<div class="im"><br>
<br>
It seems the naming convention of ions.itp is different than that of protein.top and protein-solvent.pdb. I changed protein.top and <br>
</div></blockquote>
<br>
What was your exact genion command? If you tell genion to use "-pname NA+" (which is wrong) you get this result. Note that the error says the moleculetype "NA+" is not found; the moleculetype name is "NA" instead.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
protein-solvent.pdb to match the naming of ions.itp. Then when I run grompp I get the error:<br></div>
/ERROR 1 [file protein.top, line 7228]:<div class="im"><br>
ERROR: One of the box lengths is smaller than twice the cut-off length.<br></div>
Increase the box size or decrease rlist./<div class="im"><br>
The puzzling thing is that line 7228 of protein.top is the last line of the file, that is,<br>
CL 23<br>
So the error message is not much help :(<br>
</div></blockquote>
<br>
The problem comes from the coordinate file and settings of the .mdp file; they are somehow incompatible such that they would cause a violation of the minimum image convention. Why the error points to the .top I cannot say.<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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