[gmx-users] Index file

[Shima Arasteh]

I used genconf and got a new gro file. Then I saw the ions are not recognized because of the same numbering of ions with last SOL molecules. Therefore, I changed them manually, so the problem was solved.
Thanks for your suggestions dear Justin. 
Happy New Year! 
 

Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: 
Sent: Monday, December 31, 2012 8:37 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 11:58 AM, Shima Arasteh wrote:
> 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!
>

It could be that both your last SOL and both CL ions have the same residue 
number.  Renumber the file with genconf and try again.  The only other thing I 
can think of is that you don't have an entry for CL in residuetypes.dat 
indicating that it is an ion.  The "Ion" group should be generated by default 
whenever an ion is encountered, but you don't have one.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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