<font color="#000099">Dear </font><span style="color: rgb(0, 0, 153);" class="go">Tsjerk,</span><br><font color="#000099"><br>I never thought I was being rude, probably because I was upset </font><font color="#000099">at the time</font><font color="#000099">. I apologize.<br>
<br>Unfortunately, </font><font color="#000099">I believe you'll get more of the same in the future </font><font color="#000099">if
you don't spend more time updating your page. Devilish details like Na or Na+ have no place in a tutorial. There will
be ample time later for these, when one has to fence with his own
projects.<br>
<br>Thanks for updating the tutorial.<br><br>Best regards,<br clear="all"></font><span style="color:rgb(0,0,153)">Jose</span><br>
<br><br><div class="gmail_quote">On Thu, Dec 8, 2011 at 4:11 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Jose,<br>
<br>
The references to NA+ and CL- have been changed, you can reload the<br>
page in your browser if you care to continue. Now I still think your<br>
statement was rather rude and showing disrespect to the time I put in<br>
the tutorial. Apart from the reference to NA/CL you're also factually<br>
incorrect in your statements. The first sentence of the second<br>
paragraph under the heading 'Hands on ...' (top of the page) reads:<br>
<br>
"""<br>
This tutorial uses Gromacs (<a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a>) version 4.5 and<br>
most of the commands given are specific to this package.<br>
"""<br>
<br>
Later on that page, considering the addition of ions to the topology<br>
there is the statement:<br>
<br>
"""<br>
Note the numbers of ions added, and verify that an excess of sodium<br>
ions is added for neutralization. Having replaced a number of water<br>
molecules with ions, the system topology in protein.top is not correct<br>
anymore. Edit the topology file and decrease the number of solvent<br>
molecules. Also add a line specifying the number of NA ions and a line<br>
specifying the amount of CL.<br>
"""<br>
<br>
You may note I changed NA+ to NA and CL- to CL, but for the rest the<br>
paragraph was not edited or added.<br>
<br>
Although I feel personally addressed, I can add that you're not the<br>
first to respond to the tutorial like this. It is common behaviour for<br>
a subset of undergrad students that had to follow this course as part<br>
of their curriculum. And the default answer is usually one of "read",<br>
"read again" or "read better!".<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Wed, Dec 7, 2011 at 8:29 PM, Jose Borreguero <<a href="mailto:borreguero@gmail.com">borreguero@gmail.com</a>> wrote:<br>
> This tutorial doesn't seem to be quite useful, if so many errors pop up.<br>
> Maybe it was implemented for Gromacs < 4.5.x but there's no info on the<br>
> version it should be used.<br>
><br>
> However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x<br>
> tutorials :D<br>
> (<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a>)<br>
> I'll give a try with the Lyzosyme one!<br>
><br>
> - Jose<br>
><br>
><br>
> On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>
>><br>
>><br>
>> Jose Borreguero wrote:<br>
>>><br>
>>> Hi Justin, thanks for your reply!<br>
>>><br>
>>> I appended '-p protein.top' to genion. File protein.top was automatically<br>
>>> updated by insertion of the following lines at the end of the file:<br>
>>> /[ molecules ]<br>
>>><br>
>>> ; Compound #mols<br>
>>> Protein_chain_A 1<br>
>>> SOL 7791<br>
>>> NA+ 26<br>
>>> CL- 23/<br>
>>><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>
>>> /Fatal error:<br>
>>> No such moleculetype NA+/<br>
>>><br>
>>><br>
>>> I checked file gromos45a3.ff/ions.itp. The sodium is included in this<br>
>>> fashion:<br>
>>> /[ moleculetype ]<br>
>>><br>
>>> ; molname nrexcl<br>
>>> NA 1<br>
>>> [ atoms ]<br>
>>> ; id at type res nr residu name at name cg nr charge mass<br>
>>> 1 NA+ 1 NA NA 1 22.9898/<br>
>>><br>
>>><br>
>>> It seems the naming convention of ions.itp is different than that of<br>
>>> protein.top and protein-solvent.pdb. I changed protein.top and<br>
>><br>
>><br>
>> What was your exact genion command? If you tell genion to use "-pname<br>
>> NA+" (which is wrong) you get this result. Note that the error says the<br>
>> moleculetype "NA+" is not found; the moleculetype name is "NA" instead.<br>
>><br>
>>> protein-solvent.pdb to match the naming of ions.itp. Then when I run<br>
>>> grompp I get the error:<br>
>>> /ERROR 1 [file protein.top, line 7228]:<br>
>>><br>
>>> ERROR: One of the box lengths is smaller than twice the cut-off length.<br>
>>> Increase the box size or decrease rlist./<br>
>>><br>
>>> The puzzling thing is that line 7228 of protein.top is the last line of<br>
>>> the file, that is,<br>
>>> CL 23<br>
>>> So the error message is not much help :(<br>
>><br>
>><br>
>> The problem comes from the coordinate file and settings of the .mdp file;<br>
>> they are somehow incompatible such that they would cause a violation of the<br>
>> minimum image convention. Why the error points to the .top I cannot say.<br>
>><br>
>><br>
>> -Justin<br>
>><br>
>> --<br>
>> ========================================<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">(540) 231-9080</a><br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>> ========================================<br>
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><br>
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<br>
<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</font></span><div class="HOEnZb"><div class="h5">--<br>
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