[gmx-users] Index file

Luis Felipe Pineda de Castro luis.pinedadecastro at lnu.se
Mon Dec 31 19:11:56 CET 2012

A good minded advice Shima: think more for your self; science is not easy, or if it's not possible, ask ur adviser, or look for a new job.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Shima Arasteh [shima_arasteh2001 at yahoo.com]
Sent: Monday, December 31, 2012 5:58 PM
To: Justin Lemkul; Discussion list for GROMACS users
Subject: Re: [gmx-users] Index file

These are the last line of my gro file:

    5SOL    HW299818   7.429   8.372  11.524
    5CL      CL99819   0.485   3.864  11.451
    5CL      CL99820   5.689   6.730   9.692
   9.21490   8.92980  12.40750

Here, I brought you the output of make_ndx command. As you see CL ions are not recognized here.

 Analysing residue names:
There are:    48    Protein residues
There are:   238      Other residues
There are: 12624      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

  0 System              : 99817 atoms
  1 Protein             :   720 atoms
  2 Protein-H           :   356 atoms
  3 C-alpha             :    48 atoms
  4 Backbone            :   144 atoms
  5 MainChain           :   190 atoms
  6 MainChain+Cb        :   234 atoms
  7 MainChain+H         :   240 atoms
  8 SideChain           :   480 atoms
  9 SideChain-H         :   166 atoms
 10 Prot-Masses         :   720 atoms
 11 non-Protein         : 99097 atoms
 12 Other               : 31892 atoms
 13 POPC                : 31892 atoms
 14 Water               : 67205 atoms
 15 SOL                 : 67205 atoms
 16 non-Water           : 32612 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

Somehow confusing for me!


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, December 31, 2012 8:19 PM
Subject: Re: [gmx-users] Index file

On 12/31/12 11:45 AM, Shima Arasteh wrote:
> It is 4.5.5.
> I need to say that I had a pdb file which was produced by VMD, May it be the reason of problem?

Without seeing the aforementioned information (substituting make_ndx screen output for editconf command, which is not relevant), it's impossible to say anything.  There is no logical reason why ions present in the coordinate file (independent of format) do not show up in the selection list and I cannot reproduce the problem with any file I have available.  Ions are showing up just fine in everything I can see.


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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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