[gmx-users] Usage of g_spatial

[Venkat Reddy]

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.neale at 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
> --
> --
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-- 
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.neale at 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 at 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-request at 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