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 http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it
will help.
________________________________
From: Anushree Tripathi <anushritripa...@gmail.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Wednesday, February 1, 2012 10:34 AM
Subject: [gmx-users] problem with make_ndx
When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing
the following options:
0 System : 18379 atoms
1 Protein : 11739 atoms
2 Protein-H : 9135 atoms
3 C-alpha : 1173 atoms
4 Backbone : 3519 atoms
5 MainChain : 4693 atoms
6 MainChain+Cb : 5773 atoms
7 MainChain+H : 5842 atoms
8 SideChain : 5897 atoms
9 SideChain-H : 4442 atoms
10 Prot-Masses : 11739 atoms
11 non-Protein : 6640 atoms
12 Water : 6636 atoms
13 SOL : 6636 atoms
14 non-Water : 11743 atoms
15 Ion : 4 atoms
16 CL : 4 atoms
17 Water_and_ions : 6640 atoms
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:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp.
In that case use the '-n' option.
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
[DPPC]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50
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:
Atom 1 in multiple T-Coupling groups (1 and 2).
Please suggest me the reason as well as solution for this problem.
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