Use solvent group (Group 13) for neutralization.<br><br>Pawan <br><br><div class="gmail_quote">On Sat, May 9, 2009 at 5:03 PM, nitu sharma <span dir="ltr"><<a href="mailto:sharmanitu35@gmail.com">sharmanitu35@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear all,<br><br> Thanks for solving lot of problem of me in doing membrane membrane protein simulation. Now I have a one problem I want to add ion to the my system by genion command <br>
<br>for this i am following justin's tutorial but in the genion step when i have put the command like this -<br>
genion -s ions.tpr -o compsol-ions.gro -p topol1.top -pname NA+ -nname CL- -np 1 <br> and I choose the 0 for adding ions to the system then I have got the error like this -<br><br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
Group 0 ( System) has 598751 elements<br>Group 1 ( Protein) has 9902 elements<br>Group 2 ( Protein-H) has 7778 elements<br>Group 3 ( C-alpha) has 1000 elements<br>Group 4 ( Backbone) has 3000 elements<br>
Group 5 ( MainChain) has 4000 elements<br>Group 6 (MainChain+Cb) has 4922 elements<br>Group 7 ( MainChain+H) has 4961 elements<br>Group 8 ( SideChain) has 4941 elements<br>Group 9 ( SideChain-H) has 3778 elements<br>
Group 10 ( Prot-Masses) has 9902 elements<br>Group 11 ( Non-Protein) has 588849 elements<br>Group 12 ( DMPC) has 5520 elements<br>Group 13 ( SOL) has 583329 elements<br>Group 14 ( Other) has 588849 elements<br>
Select a group: 0<br>Selected 0: 'System'<br><br>-------------------------------------------------------<br>Program genion, VERSION 4.0.3<br>Source code file: gmx_genion.c, line: 443<br><br>Fatal error:<br>Your solvent group size (598751) is not a multiple of 8<br>
-------------------------------------------------------<br><br>can any suggest me what should I do to solve this problem . I am doing first time all these these things so if anyone can suggest me something I will be really thankful for him/her.<br>
<br>Thanks a lot.<br><font color="#888888"><br>Nitu Sharma<br>School of life sciences<br>Jawaherlal nehru university<br>New delhi, india<br><br>
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