[gmx-users] problem with make_ndx

[Kowsar Bagherzadeh]

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 <anushritripathi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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.

-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120201/9382dd9f/attachment.html>