Re: [gmx-users] problem with make_ndx
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
Re: [gmx-users] problem with make_ndx
Anushree Tripathi wrote: 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 If there's no CL ions (and you suspect there should be), then you've passed make_ndx a coordinate file that does not have CL in it. Be careful with file names and use a text editor to examine the contents. 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. This error again suggests that you have not kept track of the contents of your coordinate file and/or topology and they now are not in sync with one another. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] problem with make_ndx
You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it will help. From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 10:34 AM Subject: [gmx-users] problem with make_ndx 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 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 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 listgmx-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
Re: [gmx-users] problem with make_ndx
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] 123456789 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 listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] problem with make_ndx
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] 123456789 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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] problem with make_ndx
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.auwrote: 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.auwrote: 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] 123456789 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] problem with make_ndx
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.auwrote: 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.auwrote: 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] 123456789 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] problem with make_ndx
On 2/02/2012 5:41 PM, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. Start here http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations, as I think Justin already suggested. You should definitely learn (about) other people's workflows before attempting to adapt them to your needs. Mark On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.au mailto: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 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] 123456789 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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with make_ndx
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] 123456789 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] problem with make_ndx
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] 123456789 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
Re: [gmx-users] problem with make_ndx
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] 123456789 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 listgmx-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
Re: [gmx-users] problem with make_ndx
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: ;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. On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: 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] 123456789 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 listgmx-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 listgmx-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
