Re: [gmx-users] hello
On 18/06/2012 7:46 PM, Anik Sen wrote: Hi This is Anik. Please choose an email subject more descriptive of your problem. That's your chance to attract attention! Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The DNA consisted of a total 10 base pairs. But within the simulation the DNA is moving inside the solvation box and sometimes it is going outside of the box, though due to NVT simulation criteria the part going out from one side comes back from the other side. But the problem is in a certain step it looks awkward that part of DNA lying here and part lying there. I have taken bigger boxes but with the same result. Can anyone suggest how to overcome this problem? The interaction of the DNA with the water molecules may not hamper but it may not dance so much in the solvation box. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- 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] hello
On 6/18/12 5:46 AM, Anik Sen wrote: Hi This is Anik. Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The DNA consisted of a total 10 base pairs. But within the simulation the DNA is moving inside the solvation box and sometimes it is going outside of the box, though due to NVT simulation criteria the part going out from one side comes back from the other side. But the problem is in a certain step it looks awkward that part of DNA lying here and part lying there. I have taken bigger boxes but with the same result. Can anyone suggest how to overcome this problem? The interaction of the DNA with the water molecules may not hamper but it may not dance so much in the solvation box. This topic seems to come up every day. Consult the following page and/or the many recent threads in the list archive: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Hello
On 11/01/2012 5:27 PM, Nirmal Prasad wrote: Dear Mark, I am facing problem in creating Heme topology...prodrg server is showing error , This is a GROMACS mailing list, so we're generally unable to help with that. We certainly can't help if you don't tell us details about the error. can you please tell how to solve this problem or can you please provide the heme topology No. I do not know anything about heme topologies. People will be much more likely to help if they can see you working actively on your own problem. What forcefields have been successfully used for modelling heme groups in the past? How did they generate topologies? Mark here are the PDB coordinates for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal On 1/10/12, Nirmal Prasadnimmynir...@gmail.com wrote: Dear Mark, Thank you very much..now its working nirmal On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a functional PATH. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation . Mark nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Hello
Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. nirmal On Mon, Jan 9, 2012 at 1:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/01/2012 6:54 PM, Nirmal Prasad wrote: Dear Mark, Thanks for responding. I am new to Gromacs. I am working on Cytochrome P 450 proteins, these proteins contain HEME group. For MD run should I prepare separate protein and HEME group topologies and reconstruct protein-HEME complex. Is this procedure is correct or not. A [moleculetype] cannot have covalent bonds with atoms outside itself. So whether your HEME group bonds covalently determines what can be found in a [moleculetype]. Mark nirmal On 1/9/12, Mark Abrahammark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 9/01/2012 6:42 PM, Nirmal Prasad wrote: Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. What do you mean by treating as a ligand? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Hello
On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrc for tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- 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] Hello
I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- 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] Hello
On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a functional PATH. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation. Mark nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrc for tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- 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] Hello
Dear Mark, Thank you very much..now its working nirmal On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a functional PATH. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation . Mark nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- 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] Hello
Dear Mark, I am facing problem in creating Heme topology...prodrg server is showing error , can you please tell how to solve this problem or can you please provide the heme topology here are the PDB coordinates for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal On 1/10/12, Nirmal Prasad nimmynir...@gmail.com wrote: Dear Mark, Thank you very much..now its working nirmal On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 10:37 PM, Nirmal Prasad wrote: I got this message pdb2gmx: command not found but I installed gromacs..how to solve this error You need a functional PATH. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation . Mark nirmal On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:12 PM, Nirmal Prasad wrote: Dear Gromacs users... I am new to gromacs... I have not understood this In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor tcsh) you should use a command analogous to: source /usr/local/gromacs/bin/GMXRC near the end of that file. can any one please tell me what is this.. I answered this question about two hours ago :) Consult the link that the page you quote suggests you read. Mark -- 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!
Re: [gmx-users] Hello
On 9/01/2012 6:54 PM, Nirmal Prasad wrote: Dear Mark, Thanks for responding. I am new to Gromacs. I am working on Cytochrome P 450 proteins, these proteins contain HEME group. For MD run should I prepare separate protein and HEME group topologies and reconstruct protein-HEME complex. Is this procedure is correct or not. A [moleculetype] cannot have covalent bonds with atoms outside itself. So whether your HEME group bonds covalently determines what can be found in a [moleculetype]. Mark nirmal On 1/9/12, Mark Abrahammark.abra...@anu.edu.au wrote: On 9/01/2012 6:42 PM, Nirmal Prasad wrote: Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. What do you mean by treating as a ligand? Mark -- 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] Hello
On 9/01/2012 6:42 PM, Nirmal Prasad wrote: Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. What do you mean by treating as a ligand? Mark -- 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] Hello
Dear Mark, Thanks for responding. I am new to Gromacs. I am working on Cytochrome P 450 proteins, these proteins contain HEME group. For MD run should I prepare separate protein and HEME group topologies and reconstruct protein-HEME complex. Is this procedure is correct or not. nirmal On 1/9/12, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/01/2012 6:42 PM, Nirmal Prasad wrote: Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. What do you mean by treating as a ligand? Mark -- 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] Hello
pawan raghav wrote: I am attaching the config file which is generated on my system by using fftw-2.1.5. Please notify me where is the mistake. For future reference, ZIP archives can be inconvenient for some users (we use primarily Mac and Linux systems). There is no need to zip up a log file, just paste its text in the message. That said, there is nothing useful in the attached file. You earlier said there were problematic messages when you ran make. The output is from configuration. If you want help, you have to provide the right information. I asked about the exact error messages, taken from terminal output (or a log file, if you are saving one) that occur during compilation (the make step). There may not be anything wrong; your last message said that GROMACS compiled without a problem, so I don't fully understand what your question or concern is. -Justin -- Pawan Kumar Raghav ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
Re: [gmx-users] Hello
I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ?? Regards, Nikhil From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 14 July, 2009 12:07:24 PM Subject: Re: [gmx-users] Hello nikhil damle wrote: I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given for energy minimization. What could be possible reasons for such flying away of the peptide ? How should I fix the problem ? Please use a descriptive subject line, not a generic greeting. You are probably seeing a periodicity artefact. See http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Hello
nikhil damle wrote: I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So? You need to compare that with pre-simulation... So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ?? Try trjconv like my link suggested. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Hello
So the problem is that .tpr file has peptide shifted in another box as after g_rms with -pbc option, RMSD is still ~1.5A = .tpr file generated from .mdp file during grompp programme, has peptide away from its usual position. I am giving pbc = xyz in .mdp file as well. Why then .tpr file should have peptide displaced ? Regards, Nikhil From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 14 July, 2009 12:28:05 PM Subject: Re: [gmx-users] Hello nikhil damle wrote: I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So? You need to compare that with pre-simulation... So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ?? Try trjconv like my link suggested. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Hi Nehme, Also, in our zinc finger models, the zinc plays a structural role and it is not implicated in DNA recognition. Furthermore, I will read your paper and the references. I looked in the Literature and from NMR studies/X-ray and MD done on zinc fingers containing a zinc ion coordinated to 4 cysteines. It seems that these cysteines are deprotonated and the remaining negative charges are stabilized by nearby positively charged side chains of arginines or lysines. It's hard, although not impossible, to assess the protonation state of such a center experimentally. Mind that crystal structures and NMR structures also use force fields and predefined topologies to model the structure. That means that you will only get out what you put in. If you set some group to be deprotonated while it should be protonated, this may be hard or even impossible to track down. You may still get a reasonable fit to the experimental data. For such issues Xray/NMR are not the best means. Note that I'm not saying you're wrong, but you should justify your choices. I tried to use CHARMM forcefield, but every time I had the 4 cysteines protonated, the coordination bonds removed and the parameters for zinc not assigned. How can I solve this issue? In Gromacs you can use the file specbond.dat to define special bonds. Have a look at http://wiki.gromacs.org/index.php/specbond.dat and search the archives for more information. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Hi Nehme, I've did simulations on TRAIL, which also contains a zinc-finger domain, involving three cysteines and a chloride ion. But it's not so simple. Luckily the exact parameters seemed not that vital, as the zinc apparently functions to keep the three subunits together and was in any case not directly related to the properties we were interested in. Still, I spent some time parameterizing it. For that I did quite a search of the available literature. You'll find some references in our 2008 Proteins paper. One of the most striking things is the still unresolved issue of the protonation state of zinc finger domains. Especially in the acidic environment around DNA, this may become an issue. It is why I have stayed away from zinc-finger domains lately, as they'd cost me too much work properly parameterizing them, even though our lab is doing experimental work on them and it would be interesting to complement that with MD. That's also why I mentioned to be interested in such parameters. Not in what you can readily calculate with QM or what you can get from automatic topology builders or even from literature, including my own. That doesn't solve the issue of the protonation state or overall charge of the complex. I won't trust any report on zinc-finger domain MD, unless it is shown to properly reproduce experimental properties, including what can be determined in relation to the protonation state. Cheers, Tsjerk On Wed, May 20, 2009 at 10:40 AM, Nehme El Hachem n...@aub.edu.lb wrote: Hi Tsjerk, I thank you for your help. Indeed, I am very new to GROMACS ( I have a Linux Red hat 9.0 and I do have some issues installing the software). If you are interested, please find a link: http://www.epress.com/w3jbio/vol2/harris2/harris.htm Molecular Dynamics Simulation Of The Estrogen Receptor Protein In Complex With A Non-Consensus Estrogen Response Element DNA Sequence In A 10 Angstrom Water Layer. I am trying to do some molecular dynamics on the oestrogen receptor DNA binding domain (PDB code: 1HCQ). I have InsightII with Discover3 and CHARMm but I am confused with the type of forcefield that I need. Furthermore, I have to add counterions to neutralize the system, so it seems complicated. I wanted to try GROMACS, because it has many forcfields (ex: ffAmber) for modeling this type of system. I appreciate your help, Nehme. -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Nehme El Hachem wrote: Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? The first step is probably to search in the literature for anything similar. Has anyone attempted such work? Is there precedent for making the force field choice? The only force field I know of that contains deprotonated cysteine that has also been implemented in Gromacs is AMBER (residue CYM). The ffamber ports are available for download online. Another thing to consider is whether any MM force field will adequately describe your coordination complex, i.e.: http://wiki.gromacs.org/index.php/Exotic_Species -Justin I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Nehme ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Hi, Have a look at http://wiki.gromacs.org/index.php/Parameterization and http://wiki.gromacs.org/index.php/Exotic_Species Next to that, also consider that you are talking about a site with -2 formal charge (ZnS4)2-. How likely is that? From QM studies, it seems much more likely that there are 1 or 2 protons associated with the cluster. If you manage to model that properly, let me know; I'd be interested in that. Cheers, Tsjerk On Tue, May 19, 2009 at 2:01 PM, Nehme El Hachem n...@aub.edu.lb wrote: Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Nehme ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Hello
Hi Anamika, It would be good to do some background reading on MD. For this issue, you most likely should read: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Cheers, Tsjerk On Feb 12, 2008 11:14 AM, Anamika Awasthi [EMAIL PROTECTED] wrote: Dear Gromacs users, I am beginner in using using GROMACS and MD simulations, Please help me in solving my problem. I simulate my protein for 5 ns and after simulations RMSD in C-alpha is showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and again its showing fluctuation its till 2.5 nm. Please Tell me how should I analyze this and How can I sort out this problem. Thanking you -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hello
Quoting Anamika Awasthi [EMAIL PROTECTED]: Dear Gromacs users, I am beginner in using using GROMACS and MD simulations, Please help me in solving my problem. I simulate my protein for 5 ns and after simulations RMSD in C-alpha is showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and again its showing fluctuation its till 2.5 nm. Please Tell me how should I analyze this and How can I sort out this problem. There are a few things you can do to help us help you. This message does not provide much useful information. 1. Provide an appropriate subject for your email to draw the attention of someone who might be interested. 2. Describe your system. I would not be surprised if you get strange results from simulating a protein at 800K, using a broken topology. So what is it that you are doing? Did grompp give you any error messages that you conveniently ignored? It might also be helpful to show us your .mdp file. When posting to a list like this one, try to be as explicit as possible. If you a get a strange result, and that's all you tell us, we can only guess wildly at the problem. Also, as a general reference for a newcomer to Gromacs and MD, have a look at: http://wiki.gromacs.org/index.php/Beginners -Justin Thanking you -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] HELLO
On Tue, 11 Dec 2007 04:54:51 -0800 (PST) Farzad Molani [EMAIL PROTECTED] wrote: Hi dear I'm going to compute PMF for two amins by free energy perturbation but I don't know what do I? please help me. check the tutorials ... thanks in advance. - Never miss a thing. Make Yahoo your homepage. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
