[gmx-users] On creating pdb file using dynamic indices from g_select

Mr Bernard Ramos bgrquantum at yahoo.com
Sat Sep 1 22:03:10 CEST 2012

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..



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