[gmx-users] Using make_ndx

[Justin A. Lemkul]

Lili Peng wrote:
> Hi everyone,
> 
> I'm trying to figure out the right commands for make_ndx so to generate 
> the correct index.ndx file for g_bond analysis.  From my PDB file:
> 
> ATOM      1  BN0 GGA X   1     107.255  17.133  66.368  1.00  0.00      
> P1   C
> ATOM      2  SC1 GGA X   1     110.304  14.942  66.116  1.00  0.00      
> P1   C
> ATOM      3  SC2 GGA X   1     113.632  15.318  65.904  1.00  0.00      
> P1   C
> ATOM      4  SC3 GGA X   1     114.063  12.624  65.310  1.00  0.00      
> P1   C
> ATOM      5  BN0 GGA X   2     108.171  20.156  68.028  1.00  0.00      
> P1   C
> ATOM      6  SC1 GGA X   2     109.535  18.753  71.242  1.00  0.00      
> P1   C
> ATOM      7  SC2 GGA X   2     112.445  17.547  72.396  1.00  0.00      
> P1   C
> ATOM      8  SC3 GGA X   2     111.301  16.592  74.758  1.00  0.00      
> P1   C
> ATOM      9  BN0 GGA X   3     110.843  21.726  66.258  1.00  0.00      
> P1   C
> ATOM     10  SC1 GGA X   3     111.984  24.201  68.852  1.00  0.00      
> P1   C
> ATOM     11  SC2 GGA X   3     114.049  24.264  71.496  1.00  0.00      
> P1   C
> ATOM     12  SC3 GGA X   3     113.142  26.763  72.351  1.00  0.00      
> P1   C
> ...<rest of PDB file not included>...
> 
> Say I want to group together atoms SC1, SC2, and SC3 from all GGA 
> residues in make_ndx:
> 
>   0 System              : 19699 atoms
>   1 GGA                 :   472 atoms
>   2 DRG                 :   324 atoms
>   3 W                   : 18669 atoms
>   4 ION                 :   234 atoms
> 
> I typed in:
> 
>  > r GGA & t SC1 | r GGA & t SC2 | r GGA & t SC3
> 
> Found 472 atoms with residue name GGA
> Found 36 atoms with type SC1
> Merged two groups with AND: 472 36 -> 0
> Found 472 atoms with residue name GGA
> Merged two groups with OR: 0 472 -> 472
> Found 24 atoms with type SC2
> Merged two groups with AND: 472 24 -> 0
> Found 472 atoms with residue name GGA
> Merged two groups with OR: 0 472 -> 472
> Found 0 atoms with type SC3
> 
>   5 GGA_&_SC1_GGA_&_SC2_GGA:   472 atoms
> 
> However,  make_ndx "found 0 atoms with type SC3".  I'm not sure if I'm 
> doing this correctly. 
> 

You're not, or else it would have worked :)

Better approach:

r GGA & a SC1 SC2 SC3

In order to specify atom *types* you must be using a run input file (.tpr), and 
SC1, SC2, and SC3 are atom *names* in the .pdb file, but not necessarily their type.

-Justin

> If anyone has any insight, I would be most appreciative.
> 
> Thanks,
> L
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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