Anushree Tripathi wrote:
But in coordinate file(.pdb file) ,I am not getting the atoms which
belongs to DPPC.only I have included the name of dppc.itp file like this:
This is precisely the problem - you have no DPPC in the coordinate file.
;Include DPPC chain topology
#include "dppc.itp"
Adding information to the topology has no effect on the coordinate file.
Consult the membrane protein tutorial for how to properly build such a system.
http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
-Justin
That's why I have found the atoms wich belongs to DPPC molecule from
dppc.itp file itself.
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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