[gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

I want to calculate water SDF around C-alpha of glycine molecule. So here i
have followed the commands..
Step 2:- gmx trjconv -s nptmd.tpr -f nptmd.xtc -o abc.tng -boxcenter tric
-ur compact -pbc none
and it asks me
Select group for output
Group     0 ( System) has  1543 elements
Group     1 ( Protein) has    10 elements
Group     2 ( Protein-H) has     5 elements
Group     3 ( C-alpha) has     1 elements
Group     4 ( Backbone) has     3 elements
Group     5 ( MainChain) has     3 elements
Group     6 ( MainChain+Cb) has     3 elements
Group     7 ( MainChain+H) has     6 elements
Group     8 ( SideChain) has     4 elements
Group     9 ( SideChain-H) has     2 elements
Group    10 (Prot-Masses) has    10 elements
Group    11 (non-Protein) has  1533 elements
Group    12 ( Water) has  1533 elements
Group    13 ( SOL) has  1533 elements
Group    14 ( non-Water) has    10 elements
and i have selected Group 0 (System),
Step3:- gmx trjconv -s nptmd.tpr -f abc.tng -o def.tng -fit rot+trans
Select group for least squares fit Group 0 ( System) has 1543 elements
Group 1 ( Protein) has 10 elements Group 2 ( Protein-H) has 5 elements
Group 3 ( C-alpha) has 1 elements Group 4 ( Backbone) has 3 elements Group
5 ( MainChain) has 3 elements Group 6 ( MainChain+Cb) has 3 elements Group
7 ( MainChain+H) has 6 elements Group 8 ( SideChain) has 4 elements Group 9
( SideChain-H) has 2 elements Group 10 ( Prot-Masses) has 10 elements Group
11 ( non-Protein) has 1533 elements Group 12 ( Water) has 1533 elements
Group 13 ( SOL) has 1533 elements Group 14 ( non-Water) has 10 elements
If i give group 3 (since it has C-alpha atoms), but i am getting an error as
Fatal error: Need at least 2 atoms to fit!

So, how can i solve this issue..?? since C-alpha is only one atom..

Thank you.


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On Tue, Apr 3, 2018 at 2:25 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> I want to do the Spatial Distribution Function,
> I tried to follow the manual gmx spatial.....
> I am following the five-step protocol which is given in gmx spatial
> manual..
> 1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
> the Ow's of water molecules, Is this index good or should i have all the
> molecules..??)
> 2) in the second step-  "gmx trjconv -s a.tpr
> <http://manual.gromacs.org/online/tpr.html> -f a.tng
> <http://manual.gromacs.org/online/tng.html> -o b.tng
> <http://manual.gromacs.org/online/tng.html> -boxcenter tric -ur compact
> -pbc none" here we need to give the input file ie., -f a.tng from where
> does this .tng file i need to give the input..?? How do i create a .tng
> file.. what information does this tng file contain...??
>
> Any suggestions...
>
> Thank you.
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> ‌
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student