[gmx-users] problem with make_ndx
Anushree Tripathi
anushritripathi at gmail.com
Sun Feb 5 14:37:06 CET 2012
Now, for making the index file it is showing option for DPPC but not for
Cl.The options which I found after running the command( i.e.,
make_ndx -f em.gro -o index.ndx)are given below:
0 System : 17365 atoms
1 Other : 6400 atoms
2 DPPC : 6400 atoms
3 Water : 10965 atoms
4 SOL : 10965 atoms
5 non-Water : 6400 atoms
After following each and every step that you have given,when I run the
command ( grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndp -o
nvt.tpr).I am getting error:
number of coordinates in coordinate file (em.gro, 17365)
does not match topology (topol.top, 18379)
Please guide me.
On Thu, Feb 2, 2012 at 12:58 PM, Peter C. Lai <pcl at uab.edu> wrote:
> Ok. You will:
>
> 1. Need an actual DPPC bilayer. You can either make one from scratch (using
> something like VMD), or use pre-equilibrated patches from other people
> (like
> the ones from
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
> (dppc128.pdb from that site).
>
> 2a. The bilayer and parameters by itself should be able to pass a simple
> grompp energy minimization mdp file without any errors (notifications are
> ok).
>
> Practice making a .top file with forcefield.itp, dppc.itp , lipid.itp,
> spc.itp and [ molecules ] section with the # of lipid molecules in the
> lipid-only .gro file.
> Then take a simple em.mdp and try to run grompp using your .top file and
> .gro file.
>
> 2b. Make sure your protein is properly parameterized. It too should be able
> to pass a grompp simple energy minimization preprocessing without any fatal
> errors by itself.
>
> 3. A way to insert your membrane protein into the bilayer/solvent complex.
> I think Justin uses InflateGRO method but some of us use g_membed.
>
> Orient the protein to the proper coordinates within the lipid/solvent
> system, and folllow the insertion protocol. At some point you will need to
> merge the Protein, DPPC, and water atom coordinates into a single .gro file
> and also merge all of the parameters (.itp) into a single top file.
>
> As Mark said, pay attention to all everything on this page:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
>
> On 2012-02-02 12:36:54PM +0530, Anushree Tripathi wrote:
> > Yes I want to simulate the protein inside DPPC bilayer but how could I
> make
> > the index file. Everytime it is showing error that no DPPC found in
> index
> > file.
> >
> > On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai <pcl at uab.edu> wrote:
> >
> > > Are you actually trying to simulate a membrane protein inside a DPPC
> > > bilayer
> > > though? If not, what is your reason for having it in your system?
> > >
> > > Also the topol.top file does not contain coordinates at all, only the
> > > forcefield parameterization.
> > >
> > > On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote:
> > > > Please suggest me the exact way to include dppc coordinates in
> topol.top
> > > > file.
> > > >
> > > > On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <
> Mark.Abraham at anu.edu.au
> > > >wrote:
> > > >
> > > > > 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.Abraham at 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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> > > > >
> > > > >
> > > > >
> > > > >
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> > > --
> > > ==================================================================
> > > Peter C. Lai | University of Alabama-Birmingham
> > > Programmer/Analyst | KAUL 752A
> > > Genetics, Div. of Research | 705 South 20th Street
> > > pcl at uab.edu | Birmingham AL 35294-4461
> > > (205) 690-0808 |
> > > ==================================================================
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> ==================================================================
> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst | KAUL 752A
> Genetics, Div. of Research | 705 South 20th Street
> pcl at uab.edu | Birmingham AL 35294-4461
> (205) 690-0808 |
> ==================================================================
>
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