[gmx-users] position restrain

[Justin A. Lemkul]

If you read the documentation for genpr, it tells you that it will only generate
a position restraint file for the first molecule, so grompp is telling you that
only the protein is being restrained, which is what you should expect.  If you
really insist on restraining the water molecules, try reading about the
freezegrps options for your .mdp file, but doing so will typically cause
problems if you are using pressure coupling.

-Justin

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
> hi
> I have a system of protein, popc,water and Cl ions. I want to position
> restrain protein and water as without position restrain water is going into
> the membrane . So I made a group of protein and water together using make_ndx
> and then genpr. When i ran grompp i got the following error:
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1108
>
> Fatal error:
> [ file "posre1.itp", line 582 ]:
>              Atom index (5362) in position_restraints out of bounds (1-577)
>
> The commands i used are:
> make_ndx -f em_dpt_popc.gro -o
>  0 System              : 12663 atoms
>   1 Protein             :   577 atoms
>   2 Protein-H           :   456 atoms
>   3 C-alpha             :    59 atoms
>   4 Backbone            :   177 atoms
>   5 MainChain           :   237 atoms
>   6 MainChain+Cb        :   294 atoms
>   7 MainChain+H         :   296 atoms
>   8 SideChain           :   281 atoms
>   9 SideChain-H         :   219 atoms
>  10 Prot-Masses         :   577 atoms
>  11 Non-Protein         : 12086 atoms
>  12 POPC                :  4784 atoms
>  13 SOL                 :  7299 atoms
>  14 Cl                  :     3 atoms
>  15 Other               : 12086 atoms
>
>  nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>  'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>  't': atom type   |   'keep' nr        'splitat' nr    'h': help
>  'r': residue         'res' nr         'chain' char
>  "name": group        'case': case sensitive           'q': save and quit
>
> > 1|13
>
> Copied index group 1 'Protein'
> Copied index group 13 'SOL'
> Merged two groups with OR: 577 7299 -> 7876
>
>  16 Protein_SOL         :  7876 atoms
>
> > q
>
> genpr -f em_dpt_popc.gro -o posre1 -n index.ndx
>
> Group    16 ( Protein_SOL) has  7876 elements
> Select a group: 16
> Selected 16: 'Protein_SOL'
>
> grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o
> pr_dpt_popc
>
> What is the best way to do this? Please suggest.
> _________________________________________________________________
> Check out some new online services at Windows Live Ideas—so new they haven’t
> even been officially released yet.
>
http://www.msnspecials.in/windowslive/_______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================