[gmx-users] Usage of g_spatial
Sounds like a trjconv problem, not a g_spatial problem to me. You should center only the group that makes sense for your SDF -- you probably want to pick a single cation for this (then, separately, do another run selecting a single anion; each will be used to generate a separate SDF). Then output the whole system. This should work. If not, then I suggest that you start a new post with a relevant title and figure out what you are doing wrong with trjconv ... you'll need to post actual commands there with associated error messages. If you want to output only a portion of the system in your step 1, then you need to provide a -s input with the same number of atoms in step 2. Nevertheless, just use the whole system for trjconv for now since it should work. Regarding your seeing the whole distribution for ANI from g_spatial output in VMD, I don't understand what you see and what you expect/want to see. Try posting a figure somewhere online and post with its location and a description of what you want to obtain. If you want the distribution of all C cations around the average of all A anions, then you need to create a trajectory that is A times as long as your real trajectory and reorder the coordinates so that each anion has a turn being residue number N. Then center your whole trajectory about residue N. This is a hack, but it works for me and I think is what you want. Also, the tool g_sdf does this on its own so you might look online for an older version of it. I found it less useful than g_spatial for my purposes, but some users have found it to be the perfect tool. Chris. -- original message -- Yes, trjconv works without tpr. Thanks for that. I want to see the distribution of anion around cation. Is it not possible to see an averaged spatial distribution of all anions around all cations? Do I need to make a selection of a single cation molecule? I did the selection of a single cation molecule which is approximately at the center of the box and did the following step 1: trjconv -s 1md.pdb -f 11md_gro.pdb -o 11md_gro_mod.pdb -center -ur compact -pbc none when it asked for group for centering and output, I selected the whole system for both. step 2: trjconv -s 1md.pdb -f 11md_gro_mod.pdb -o 11md_gro_mod1.pdb -fit rot+trans when it asked for group for least square once again I selected the whole system I selected the whole system as a previous discussion http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html suggested the same because of an error that was happening in step 2. *Fatal error: Index[2385] 2410 is larger than the number of atoms in** the trajectory file (2409). * Since I was getting the same error if I made any form of selections in the first two steps, I output the whole system. step 3: g_spatial. and used ANI as group to generate SDF and a single cation residue as the group to output coords When I loaded the resultant cube in vmd I could see the whole distribution. Where am I going wrong? -- 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] Usage of g_spatial
Sir Yes, trjconv works without tpr. Thanks for that. I want to see the distribution of anion around cation. Is it not possible to see an averaged spatial distribution of all anions around all cations? Do I need to make a selection of a single cation molecule? I did the selection of a single cation molecule which is approximately at the center of the box and did the following step 1: trjconv -s 1md.pdb -f 11md_gro.pdb -o 11md_gro_mod.pdb -center -ur compact -pbc none when it asked for group for centering and output, I selected the whole system for both. step 2: trjconv -s 1md.pdb -f 11md_gro_mod.pdb -o 11md_gro_mod1.pdb -fit rot+trans when it asked for group for least square once again I selected the whole system I selected the whole system as a previous discussion http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html suggested the same because of an error that was happening in step 2. *Fatal error: Index[2385] 2410 is larger than the number of atoms in** the trajectory file (2409). * Since I was getting the same error if I made any form of selections in the first two steps, I output the whole system. step 3: g_spatial. and used ANI as group to generate SDF and a single cation residue as the group to output coords When I loaded the resultant cube in vmd I could see the whole distribution. Where am I going wrong? On Tue, May 7, 2013 at 6:23 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Try this: trjconv -s my.pdb -f my.pdb -o mymod.pdb g_spatial -s mymod.pdb -f mymod.pdb For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option) Chris. -- original message -- I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 On Tue, May 7, 2013 at 6:23 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Try this: trjconv -s my.pdb -f my.pdb -o mymod.pdb g_spatial -s mymod.pdb -f mymod.pdb For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option) Chris. -- original message -- I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Usage of g_spatial
Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Usage of g_spatial
I think you can process the trajectories without generating TPR. Dr. Vitaly Chaban On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote: Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Usage of g_spatial
Try this: trjconv -s my.pdb -f my.pdb -o mymod.pdb g_spatial -s mymod.pdb -f mymod.pdb For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option) Chris. -- original message -- I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- -- 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] Usage of g_spatial
Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I think you can process the trajectories without generating TPR. Dr. Vitaly Chaban On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote: Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Usage of g_spatial
See my previous response. You don't need a .tpr for trjconv (unless you are doing pbc operations). trjconv -h will also tell you that. Just use trjconv -s my.pdb Chris. -- original message -- Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help -- 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
