<br>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.,<font face="Arial"><font size="3"><pre>make_ndx -f em.gro -o index.ndx)are given below:<br>
<br> 0 System : 17365 atoms<br> 1 Other : 6400 atoms<br> 2 DPPC : 6400 atoms<br> 3 Water : 10965 atoms<br> 4 SOL : 10965 atoms<br> 5 non-Water : 6400 atoms<br>
<br>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:<br>
number of coordinates in coordinate file (em.gro, 17365)<br>
does not match topology (topol.top, 18379)<br><br>Please guide me.<br><br></pre></font></font><br><br><br><div class="gmail_quote">On Thu, Feb 2, 2012 at 12:58 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Ok. You will:<br>
<br>
1. Need an actual DPPC bilayer. You can either make one from scratch (using<br>
something like VMD), or use pre-equilibrated patches from other people (like<br>
the ones from <a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a>)<br>
(dppc128.pdb from that site).<br>
<br>
2a. The bilayer and parameters by itself should be able to pass a simple<br>
grompp energy minimization mdp file without any errors (notifications are ok).<br>
<br>
Practice making a .top file with forcefield.itp, dppc.itp , lipid.itp,<br>
spc.itp and [ molecules ] section with the # of lipid molecules in the<br>
lipid-only .gro file.<br>
Then take a simple em.mdp and try to run grompp using your .top file and<br>
.gro file.<br>
<br>
2b. Make sure your protein is properly parameterized. It too should be able<br>
to pass a grompp simple energy minimization preprocessing without any fatal<br>
errors by itself.<br>
<br>
3. A way to insert your membrane protein into the bilayer/solvent complex.<br>
I think Justin uses InflateGRO method but some of us use g_membed.<br>
<br>
Orient the protein to the proper coordinates within the lipid/solvent<br>
system, and folllow the insertion protocol. At some point you will need to<br>
merge the Protein, DPPC, and water atom coordinates into a single .gro file<br>
and also merge all of the parameters (.itp) into a single top file.<br>
<br>
As Mark said, pay attention to all everything on this page:<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html</a><br>
<div class="HOEnZb"><div class="h5"><br>
On 2012-02-02 12:36:54PM +0530, Anushree Tripathi wrote:<br>
> Yes I want to simulate the protein inside DPPC bilayer but how could I make<br>
> the index file. Everytime it is showing error that no DPPC found in index<br>
> file.<br>
><br>
> On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai <<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>> wrote:<br>
><br>
> > Are you actually trying to simulate a membrane protein inside a DPPC<br>
> > bilayer<br>
> > though? If not, what is your reason for having it in your system?<br>
> ><br>
> > Also the topol.top file does not contain coordinates at all, only the<br>
> > forcefield parameterization.<br>
> ><br>
> > On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote:<br>
> > > Please suggest me the exact way to include dppc coordinates in topol.top<br>
> > > file.<br>
> > ><br>
> > > On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
> > >wrote:<br>
> > ><br>
> > > > On 1/02/2012 6:25 PM, Anushree Tripathi wrote:<br>
> > > ><br>
> > > > But in coordinate file(.pdb file) ,I am not getting the atoms which<br>
> > > > belongs to DPPC.<br>
> > > ><br>
> > > ><br>
> > > > You cannot do anything unless you have a coordinate file that includes<br>
> > > > DPPC coordinates. I don't know how to express this any more clearly.<br>
> > > ><br>
> > > ><br>
> > > > only I have included the name of dppc.itp file like this:<br>
> > > > ;Include DPPC chain topology<br>
> > > > #include "dppc.itp"<br>
> > > ><br>
> > > > That's why I have found the atoms wich belongs to DPPC molecule from<br>
> > > > dppc.itp file itself.<br>
> > > ><br>
> > > ><br>
> > > > These numbers are not useful, as I have already explained.<br>
> > > ><br>
> > > > Mark<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
> > >wrote:<br>
> > > ><br>
> > > >> On 1/02/2012 6:04 PM, Anushree Tripathi wrote:<br>
> > > >><br>
> > > >> When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is<br>
> > > >> showing the following options:<br>
> > > >> 0 System : 18379 atoms<br>
> > > >> 1 Protein : 11739 atoms<br>
> > > >> 2 Protein-H : 9135 atoms<br>
> > > >> 3 C-alpha : 1173 atoms<br>
> > > >> 4 Backbone : 3519 atoms<br>
> > > >> 5 MainChain : 4693 atoms<br>
> > > >> 6 MainChain+Cb : 5773 atoms<br>
> > > >> 7 MainChain+H : 5842 atoms<br>
> > > >> 8 SideChain : 5897 atoms<br>
> > > >> 9 SideChain-H : 4442 atoms<br>
> > > >> 10 Prot-Masses : 11739 atoms<br>
> > > >> 11 non-Protein : 6640 atoms<br>
> > > >> 12 Water : 6636 atoms<br>
> > > >> 13 SOL : 6636 atoms<br>
> > > >> 14 non-Water : 11743 atoms<br>
> > > >> 15 Ion : 4 atoms<br>
> > > >> 16 CL : 4 atoms<br>
> > > >> 17 Water_and_ions : 6640 atoms<br>
> > > >><br>
> > > >><br>
> > > >> So your system has 18K atoms, with 11K protein and the rest solvent<br>
> > and<br>
> > > >> ions. As Justin suggested, this coordinate file does not have DPPC in<br>
> > it.<br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >> for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But<br>
> > there<br>
> > > >> is no option for DPPC (as given in tutorial we have to merge protein<br>
> > with<br>
> > > >> DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p<br>
> > topol.top -n<br>
> > > >> index.ndx -o nvt.tpr),it is showing error:<br>
> > > >><br>
> > > >> Group DPPC not found in indexfile.<br>
> > > >> Maybe you have non-default goups in your mdp file, while not using the<br>
> > > >> '-n' option of grompp.<br>
> > > >> In that case use the '-n' option.<br>
> > > >><br>
> > > >> To troubleshoot the error,I have kept one more group in index.ndx file<br>
> > > >> with number of atoms which I found from dppc.itp file(at the end of<br>
> > file)<br>
> > > >> like this<br>
> > > >><br>
> > > >> [DPPC]<br>
> > > >> 1 2 3 4 5 6 7 8 9 10 11 12 13 14<br>
> > 15<br>
> > > >> 16 17 18 19 20 21 22 23 24 25 26 27 28 29<br>
> > 30<br>
> > > >> 31 32 33 34 35 36 37 38 39 40 41 42 43 44<br>
> > 45<br>
> > > >> 46 47 48 49 50<br>
> > > >><br>
> > > >><br>
> > > >> These numbers have to reference the atom numbers in the coordinate<br>
> > file,<br>
> > > >> not the [moleculetype]. Since you've done the latter, you get the<br>
> > problem<br>
> > > >> with T-coupling groups. But go back and use a coordinate file that<br>
> > actually<br>
> > > >> has DPPC in it.<br>
> > > >><br>
> > > >> Mark<br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >> Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p<br>
> > > >> topol.top -n index.ndx -o nvt.tpr),I am getting the following error:<br>
> > > >><br>
> > > >> Atom 1 in multiple T-Coupling groups (1 and 2).<br>
> > > >><br>
> > > >> Please suggest me the reason as well as solution for this problem.<br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >> --<br>
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> > ==================================================================<br>
> > Peter C. Lai | University of Alabama-Birmingham<br>
> > Programmer/Analyst | KAUL 752A<br>
> > Genetics, Div. of Research | 705 South 20th Street<br>
> > <a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
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==================================================================<br>
Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
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</div></div></blockquote></div><br>