[gmx-users] On creating pdb file using dynamic indices from g_select
Mark.Abraham at anu.edu.au
Sun Sep 2 03:46:52 CEST 2012
On 2/09/2012 6:03 AM, Mr Bernard Ramos wrote:
> Hi everyone!
> I intend to create a trajectory file (in pdb format) of atoms dynamically indexed by g_select. However, I failed to produce the correct pdb file. Here is how I did it. Kindle help please.
> 1. I created the index file using g_select for water oxygen atoms within 0.4 nm of Atom 3
> g_select -f A.xtc -s A.tpr -select 'resname SOL name OW and within 0.4 of atomnr 3' -on X_ndx.
> The first few lines of X.ndx look like this
> [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.000 ]
> [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.200 ]
> [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.400 ]
> 685 1045
> 2. Then I went into trjconv to create a pdb of these water oxygens
> trjconv -f A.xtc -s A.tpr -o X.pdb -n X.ndx
> After keying in Enter, I see a list of the the dynamic groups that looks like the ones above. I have 10000 groups in the list corresponding to 10000 frames but within each frame having different number/indices of water oxygens. I then get a prompt asking me to "select a group". I'm not quite sure what number to type but I tried entering "0", "0 to 10000", but both gave me wrong pdb files. They dont match with the indices given in X.ndx. How do I tell Gromacs to create a pdb file for these specific atoms? And next time I use a dynamic index, what do I type Gromacs asks to "select a group"? Thanks..
No GROMACS tool can interpret this index file as a dynamic selection,
because the tool cannot map the time of a trajectory frame to the
selection in the index group. It is a feature expected in GROMACS 5.0,
but don't hold your breath. In the meantime, you will have to write a
shell script to loop over frames, applying the correct single index
group to each frame. trjconv -sep might be a good starting point.
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