Hi gmx users,<div> My system has two protein chain + solvent, and the total charge is -12. I use "genion" to add 12 Na+ in the *.tpr and *.top file.</div><div> However there is some fatal error happens when I try to regenerate the new tpr file for calculation, it really confuse me. </div>
<div> The process and error msg is below:</div><div><br></div><div> 1. genion_d -s neg_charge.tpr -nice 0 -np 12 -pname Na -rmin 0.6 -p system_neg.top -o out.gro -g genion.log</div><div> Then the topology file is updated, with some Na added. change name into system_neu.top</div>
<div><br></div><div> 2. copy ions.itp in the current folder, add #include "ions.itp" in system_neu.top</div><div> </div><div> 3. Then I use </div><div> grompp -f for_md.mdp -c out.gro -p system_neu.top -o md_run.tpr -maxwarn 1000 >& gen_tpr.log</div>
<div> try to get the new md_run.tpr.</div><div><br></div><div> The error message is: "No such moleculetype Na"</div><div> I don't know how to revise the ions.itp file, and did not revise that.</div>
<div><br></div><div> Thank you in advance!</div><div><br></div><div><br><div> <br><div><br>-- <br>Sincerely<br>=================================<br>Pan Wu<br>Graduate Student in Department of Chemistry<br>Duke University<br>
124 Science Drive<br>5301 French Family Science Center<br>
Durham, NC 27708<br>Phone: (919) 660-1583<br>=================================<br><br>
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