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 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 > -- 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 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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