<font color="#000099">Hi Justin, thanks for your reply!<br><br>I appended '-p protein.top' to genion. File </font><font color="#000099">protein.top was automatically updated by insertion of the following lines at the end of the file:</font><font color="#000099"><br>
<i>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>SOL 7791<br>NA+ 26<br>CL- 23</i><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><i>Fatal error:<br>No such moleculetype NA+</i><br><br>I checked file gromos45a3.ff/ions.itp. The sodium is included in this fashion:<br><i>[ moleculetype ]<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</i><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 protein-solvent.pdb to match the naming of ions.itp. Then when I run grompp I get the error:<br>
<i>ERROR 1 [file protein.top, line 7228]:<br> ERROR: One of the box lengths is smaller than twice the cut-off length.<br> Increase the box size or decrease rlist.</i><br>The puzzling thing is that line </font><font color="#000099">7228</font> <span style="color: rgb(0, 0, 153);">of</span> <font color="#000099">protein.top is <span style="background-color: rgb(255, 255, 255);"></span>the last line of the file, that is,<br>
CL 23</font><br><span style="color: rgb(0, 0, 153);">So the error message is not much help :(</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 11:04 AM, 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;">
<div class="im"><br>
<br>
Jose Borreguero wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users,<br>
<br>
Im new to gromacs and I'm following a tutorial (<a href="http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/" target="_blank">http://nmr.chem.uu.nl/~<u></u>tsjerk/course/molmod/</a>). Unfortunately, the tutorials doesn't say anything about how to update the topology file after using 'genion' to replace a few water molecules with ions.<br>
I manually edited the topology file and updated the number of water molecules and added the number of ions:<br>
<br>
</blockquote>
<br></div>
Using the -p flag will make all the necessary changes automatically.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
SOL 7791<br>
Na+ 26<br>
Cl- 23<br>
<br>
But then when I tried to preprocess the structure with grompp, I got an error:<br>
<br>
Fatal error:<br>
No such moleculetype Na+<br>
<br>
</blockquote>
<br></div>
Assuming you're using a new version of Gromacs (4.5.x), the naming scheme has changed. Check the ions.itp for the force field you've chosen to use to set proper names.<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>==========<span class="HOEnZb"><font color="#888888"><br>
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