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 ]
  685
[ 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.

Mark
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to