<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>i added the NA using the genion <br></span></div><div>
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<ul><li><pre class="western" style="margin-bottom: 0.2in;"><font face="Bitstream Charter, serif"><font size="3">genion -s em.tpr -o waterbox_ions.gro -np 6</font></font><font face="Bitstream Charter, serif"><font size="3"> , and i added the NA to the topology file , subtracted the water number by 6. tail </font></font><font><font><font face="Bitstream Charter, serif"><font size="3">waterbox_ions.gro</font></font></font></font><font face="Bitstream Charter, serif"><font size="3"> file have this </font></font></pre></li></ul>
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<span></span></div><div> 3567W W 3789 1.256 3.600 3.784<br> 3568W W 3790 2.491 6.539 2.341<br> 3569W W 3791 2.432 6.349 3.116<br> 3570NA NA 3792 2.677 4.903 3.617<br> 3571NA NA 3793 0.466 3.245 4.787<br> 3572NA NA 3794 6.028 4.147 2.550<br> 3573NA NA 3795 3.201 1.027 5.879<br> 3574NA NA 3796 1.677 1.849 6.641<br> 3575NA NA
3797 5.729 5.645 7.089<br></div><div>and the topology file <br></div><div>#include "martini_v2.1.itp"<br>#include "1pef.itp"<br>#include "martini_v2.0_ions.itp"<br>[ system ]<br><br>; Name<br><br>PEPTIDE F<br><br>[ molecules ]<br><br>; Compound #mols<br><br>Protein 6<br><br>W 3551<br><br>NA+6<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><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;">À :</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Envoyé le :</span></b> Mercredi 13 Juillet 2011 13h05<br><b><span style="font-weight: bold;">Objet :</span></b> Re: [gmx-users] Adding Ions<br></font><br><br><br>errabah fatima ezzahra wrote:<br>> <br>> Hi All,<br>> <br>> <br>> I have a peptide that has three positive charged amino acids (LYS) and four negative charged amino acids (GLU) consequently it is a negative peptide. is that right<br><br>Assuming typical protonation states, and further assuming that there are no other unbalanced charges in the peptides, yes.<br><br>> when i run gromacs simualtion grompp DOES NOT gave a warning: System has non-zero total charge: -6 ( i have six peptides)<br>> <br><br>Then you do not have what you think you do. Look at the topology to see what the net charge on each peptide is and determine whether or not this is what you want.<br><br>> i tried
neutralising the system, since that the peptides have an extra -1 charge per peptide.<br>> <br>> however when i did add 6 NA to the system , after running the enrgy minimization there was an error that System has non-zero total charge: -6.000000e+00<br>> <br>> so i dont understand how by adding 6 positive ions that cause the negative charge??<br>> <br><br>It can't. You've probably confused which files you're using or are misreading some output somewhere along the way. Adding six positives cannot give six negatives.<br><br>-Justin<br><br>> thank you so much for your help<br>> <br>> FZ<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"
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