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 <p...@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 <p...@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.abra...@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.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. > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> -- > > > > >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > > > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > -- > > > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > -- > > > ================================================================== > > > Peter C. Lai | University of Alabama-Birmingham > > > Programmer/Analyst | KAUL 752A > > > Genetics, Div. of Research | 705 South 20th Street > > > p...@uab.edu | Birmingham AL 35294-4461 > > > (205) 690-0808 | > > > ================================================================== > > > > > > -- > > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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