<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Ok, thanks for the advice and sorry for sending the attached file.<br></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 16:51<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>> 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>><br>> *Para:* Eduardo Oliveira <<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>><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
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