[gmx-users] Regarding calculation of Spatial Distribution Function

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 4 14:35:19 CEST 2018

```Hi,

You're asking for a rotational fit, but you can't do that to a single atom.
Fit e.g. to the protein, and then compute the SDF around the atom of
interest.

Mark

On Wed, Apr 4, 2018 at 6:08 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> 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.
>
>
> ‌
> <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&
> >
>
> 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
> > ‌
> > <https://mailtrack.io/> Sent with Mailtrack
> > <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&
> >
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
```