<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="RIGHT: auto"><SPAN style="RIGHT: auto">You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see </SPAN><A style="RIGHT: auto" href="http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf">http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf</A> , hope it will help. <BR></div>
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<DIV style="BORDER-BOTTOM: #ccc 1px solid; BORDER-LEFT: #ccc 1px solid; PADDING-BOTTOM: 0px; LINE-HEIGHT: 0; MARGIN: 5px 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; HEIGHT: 0px; FONT-SIZE: 0px; BORDER-TOP: #ccc 1px solid; BORDER-RIGHT: #ccc 1px solid; PADDING-TOP: 0px" class=hr contentEditable=false readonly="true"></DIV><B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Anushree Tripathi <anushritripathi@gmail.com><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <gmx-users@gromacs.org> <BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Wednesday, February 1, 2012 10:34 AM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> [gmx-users] problem with make_ndx<BR></FONT></DIV><BR>
<DIV id=yiv472984042>When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options:<BR> 0 System : 18379 atoms<BR> 1 Protein : 11739 atoms<BR> 2 Protein-H : 9135 atoms<BR> 3 C-alpha : 1173 atoms<BR> 4 Backbone : 3519 atoms<BR> 5 MainChain : 4693 atoms<BR> 6 MainChain+Cb : 5773 atoms<BR> 7 MainChain+H : 5842 atoms<BR> 8
SideChain : 5897 atoms<BR> 9 SideChain-H : 4442 atoms<BR> 10 Prot-Masses : 11739 atoms<BR> 11 non-Protein : 6640 atoms<BR> 12 Water : 6636 atoms<BR> 13 SOL : 6636 atoms<BR> 14 non-Water : 11743 atoms<BR> 15 Ion : 4 atoms<BR> 16 CL
: 4 atoms<BR> 17 Water_and_ions : 6640 atoms<BR><BR>for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error:<BR><BR>Group DPPC 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.<BR><BR>To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this<BR><BR>[DPPC]<BR>1 2 3 4 5 6 7 8 9 10 11 12
13 14 15<BR>16 17 18 19 20 21 22 23 24 25 26 27 28 29 30<BR>31 32 33 34 35 36 37 38 39 40 41 42 43 44 45<BR>46 47 48 49 50<BR><BR>Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error:<BR><BR>Atom 1 in multiple T-Coupling groups (1 and 2).<BR><BR>Please suggest me the reason as well as solution for this problem.<BR></DIV><BR>-- <BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org"
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