<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Ok, thanks again. That actually worked.</span></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Terça-feira, 3 de Abril de 2012 18:30<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] grompp error<br> </font> </div> <br><br><br>Eduardo Oliveira wrote:<br>> Ok, thanks for the advice and sorry for sending the attached file.<br>> <br><br>No
apology necessary; I asked for the file. I just ask that all discussion remain on the list, so that others can contribute and learn from it.<br><br>-Justin<br><br>> ------------------------------------------------------------------------<br>> *De:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *Para:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Enviadas:* Terça-feira, 3 de Abril de 2012 16:51<br>> *Assunto:* Re: [gmx-users] grompp error<br>> <br>> <br>> <br>> Eduardo Oliveira wrote:<br>> > Thanks!<br>> ><br>> <br>> Please keep the discussion on the list. From your .mdp file:<br>> <br>> tc-grps = Protein SOL<br>> <br>>
As I suspected, you're not accounting for ions in any way. You need to. Usually "Protein Non-protein" works just fine for simple systems.<br>> <br>> -Justin<br>> <br>> ><br>> > ------------------------------------------------------------------------<br>> > *De:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>> > *Para:* Eduardo Oliveira <<a ymailto="mailto:eduardobio@yahoo.com.br" href="mailto:eduardobio@yahoo.com.br">eduardobio@yahoo.com.br</a> <mailto:<a ymailto="mailto:eduardobio@yahoo.com.br" href="mailto:eduardobio@yahoo.com.br">eduardobio@yahoo.com.br</a>>>; Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54<br>> > *Assunto:* Re: [gmx-users] grompp error<br>> ><br>> ><br>> ><br>> > Eduardo Oliveira wrote:<br>> > > Hi all,<br>> > ><br>> > > After i ran grompp I've the following message:<br>> > ><br>> > > Fatal error:<br>> > > 3 atoms are non part of any of the T-coupling groups<br>> > ><br>> > > It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp<br>> > ><br>> > > genion_d -s arath_stpr.tpr
-o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top<br>> > ><br>> > > grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr<br>> > ><br>> > > Additional information: I'm running GROMACS 4.5.5<br>> > ><br>> ><br>> > What are your tc-grps? Please provide your .mdp file.<br>> ><br>> > -Justin<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]vt.edu | (540) 231-9080<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>> ><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]vt.edu | (540) 231-9080<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>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a
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<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]vt.edu | (540) 231-9080<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>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list.
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