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<div style="margin-bottom: 0in;"> <font face="Bitstream Charter, serif"><b>I am trying to do a Short
position restrained simulation so i wrote </b></font> grompp -f pr.mdp -c <font size="3"><span style="font-weight: normal;">system</span></font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">.gro</span></font></font><font size="3"><span style="font-weight: normal;">
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</font></font></font>-p file.top -o file.tpr , i added the NA+ to the pr.mdp file</div><div style="margin-bottom: 0in;">here the pr.mdp<br><span style="font-weight: bold;"></span></div><div style="margin-bottom: 0in;"><span style="font-weight: bold;">tc-grps = Protein W NA+<br>tau_t = 0.1 0.1 0.1<br>ref_t = 300 300 300<br>; Energy monitoring<br>energygrps = Protein W NA+<br></span></div><div style="margin-bottom: 0in;"><br><span style="font-weight: bold;"></span></div><div style="margin-bottom: 0in;"> but it gave me an
error :<br></div><div style="margin-bottom: 0in;"><span style="font-weight: bold;">Fatal error:<br>Group NA+ not found in indexfile.<br>Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp.<br>In that case use the '-n' option.</span></div><div style="margin-bottom: 0in;"> </div><div style="margin-bottom: 0in;"><br></div><div style="margin-bottom: 0in;">i dont have an indexfile ? </div><div style="margin-bottom: 0in;"><br></div><div style="margin-bottom: 0in;">FZ<br></div><div style="margin-bottom: 0in;">
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</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 14h11<br><b><span style="font-weight: bold;">Objet :</span></b> [gmx-users] Re: Adding Ions<br></font><br><br><br>errabah fatima ezzahra wrote:<br>> Hi Justin<br>> <br>> when i seperated the NA+ and 6 i got this error<br>> <br>> 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><br>These notes indicate that your .mdp settings are incorrect. Follow the suggesting printed.<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><br>This error is probably harmless, since you are actually using sodium and there isn't really a mismatch. The name listed in the [molecules] section must match the name specified in the corresponding [moleculetype] directive in ions.itp, with constituent residues and atoms named accordingly. In this case, ions.itp is specifying the atom name as "NA+" while your coordinate file uses "NA" instead.<br><br>> what s th difference between NA+6 And NA+ 6 .<br>> <br><br>Spacing. All lines in the [molecules] directive are read as:<br><br>(moleculetype name) (some amount of space) (number of
molecules)<br><br>Proper spacing is an absolute requirement for proper interpretation of the topology. The amount of whitespace is unimportant, but it has to be there, otherwise grompp reads a continuous string and finds that there is a moleculetype named "NA+6" that has no molecules associated with it.<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>> *À :* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Envoyé le :* Mercredi 13 Juillet 2011 13h49<br>> *Objet :* Re: Re : [gmx-users] Adding Ions<br>> <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> <mailto:<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" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><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"
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