<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Justin <br></span></div><div><br><span></span></div><div><span>when i seperated the NA+ and 6 i got this error</span></div><div><br><span></span></div><div><span>NOTE 1 [file em.mdp]:<br> For energy conservation with switch/shift potentials, rlist should be 0.1<br> to 0.3 nm larger than rcoulomb.<br><br><br>NOTE 2 [file em.mdp]:<br> For energy conservation with switch/shift potentials, rlist should be 0.1<br> to 0.3 nm larger than rvdw.<br><br>Generated 0 of the 465 non-bonded parameter combinations<br>Excluding 1 bonded neighbours molecule type 'Protein'<br>Excluding 1 bonded neighbours molecule type 'W'<br>Excluding 1 bonded neighbours molecule type 'NA+'<br>Warning: atom name 3792 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)<br>Warning: atom name 3793 in 1pef.top and
waterbox_ions.gro does not match (NA+ - NA)<br>Warning: atom name 3794 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)<br>Warning: atom name 3795 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)<br>Warning: atom name 3796 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)<br>Warning: atom name 3797 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)<br><br>WARNING 1 [file 1pef.top, line 19]:<br> 6 non-matching atom names<br> atom names from 1pef.top will be used<br> atom names from waterbox_ions.gro will be ignored<br><br>what s th difference between NA+6 And NA+ 6 .</span></div><div><br><span></span></div><div><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 13h49<br><b><span style="font-weight: bold;">Objet :</span></b> Re: Re : [gmx-users] Adding Ions<br></font><br><br><br>Justin A. Lemkul wrote:<br>> <br>> <br><br>>> i added the NA using the genion<br>>> *<br>>> <br>>> genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to the topology file , subtracted the water number by 6. tail waterbox_ions.gro file have this<br>>> 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>>> and the topology file<br>>> #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>> <br>> This looks fine. There are other things I suggested you look at; you haven't ruled out that something else went wrong along the way or that your peptide doesn't have the net charge you think it does.<br>> <br><br>Actually, no it doesn't. You don't have any space between the moleculetype name ("NA+") and the number of molecules. This line isn't being read correctly, which might be your problem, though I'm shocked that you're not getting some other error about a missing number of molecules or number of coordinates not matching the topology.<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>-- 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. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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