On 1/02/2012 6:25 PM, Anushree Tripathi wrote:
But in coordinate file(.pdb file) ,I am not getting the atoms which
belongs to DPPC.
You cannot do anything unless you have a coordinate file that includes
DPPC coordinates. I don't know how to express this any more clearly.
only I have included the name of dppc.itp file like this:
;Include DPPC chain topology
#include "dppc.itp"
That's why I have found the atoms wich belongs to DPPC molecule from
dppc.itp file itself.
These numbers are not useful, as I have already explained.
Mark
On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
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
So your system has 18K atoms, with 11K protein and the rest
solvent and ions. As Justin suggested, this coordinate file does
not have DPPC in it.
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
These numbers have to reference the atom numbers in the coordinate
file, not the [moleculetype]. Since you've done the latter, you
get the problem with T-coupling groups. But go back and use a
coordinate file that actually has DPPC in it.
Mark
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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