[gmx-users] INDEX

[Subashini .K]

Hi,


Lot of thanks.

I'll implement it in the command line.


Thanks,

Subashini.K


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Erik Marklund <erik.marklund at kemi.uu.se>
Sent: Monday, February 6, 2017 6:07 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] INDEX

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv -n your_index_file.ndx …

Kind regards,
Erik
______________________________
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 6 Feb 2017, at 13:06, Subashini .K <subashinik at hotmail.com<mailto:subashinik at hotmail.com>> wrote:

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
www.gromacs.org
This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page.



* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists>
www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them:



* 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<mailto:gmx-users-request at gromacs.org>.
gromacs.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
maillist.sys.kth.se
gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users



--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
www.gromacs.org
This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page.



* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists>
www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them:



* 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.