[gmx-users] Make an index file

[Justin A. Lemkul]

On 4/28/12 2:06 PM, Peter C. Lai wrote:
> #2
>
> Generally a good idea to keep the names consistent, however - why are you using
> POP in the coordinate file instead of POPC?

If it is a .pdb file, the standard residue name occupies 3 characters.  Many 
files (including those from Tieleman) are distributed with such names.

To the OP's original question - the commands you issue depend on what you're 
trying to achieve.  What group do you need to create?

-Justin

> --
> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
>
> Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
>
>     Dear gmx users,
>     I want to simulate POPC in water. In equilibration step, I have to make an
>     index file. But when I enter this command, I do not know to choose which
>     group to make a suitable .ndx file which matches the molecule types and
>     molecules sections in .top file .
>
>     The .top file contains these:
>
>
>     [ moleculetype ]
>     ; Name nrexcl
>     POPC 3
>     .
>     .
>     .
>     .
>     [ system ]
>     ; name
>     POPC in water
>
>     [ molecules ]
>     ; name number
>     POPC 128
>     SOL 3800
>
>
>     It is the command I enter:
>     # make_ndx -f em.gro -o index.ndx
>     0 System : 18056 atoms
>     1 Other : 6656 atoms
>     2 POP : 6656 atoms
>     3 Water : 11400 atoms
>     4 SOL : 11400 atoms
>     5 non-Water : 6656 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
>     'ri': residue index
>
>     Now, what is the correct answer? Anybody can suggest me?
>
>     Thanks in advance,
>     Shima
>     ge
>
>
>

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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