[gmx-users] solvating a protein-bilayer CG assembly

Francesco Pietra francesco.pietra at accademialucchese.it
Thu Oct 1 09:07:55 CEST 2009


I have inserted a gc pore protein into equilibrated DCCP, removed
clashes with CHIMERA, and cut-and-paste created a single pdb file for
the ensemble.  The ensemble is now made of, let me say, four layers,
in the order protein-head, W, DCC, W. Command

genbox -cp ensemble.pdb -box 11 20 11 -o ensemble+box.pdb

inserts the ensemble correctly into a box, the ensemble looking like
as described above.

Now I want to surround the whole (like with AMBER's LEAP for all-atom
work), or selectively the protein-head, in order that the latter faces
water, not vacuum, in view of MD. If I add "-cs water-1bar.300K.gro"
to the above genbox command, everything is solvated, and the protein
is placed at the corner of the new water box.

I am not so much concerned about failure to get the protein with its
DCCP bilayer at the center of the new water box, as I already got
(unchecked) suggestions how to circumvent the issue. My concern is how
to get external solvation of the starting ensemble, the same way that
LEAP operates. I came across the indication that new solvent should
have a different name (that is different from W), but the new W is
appended in the final pdb file after DPP, W, Protein, so that the
coordinates for new solvent will not change with the name.

I feel I silly entered a mental loop. There must be in GROMACS
commands to accomplish external solvation of an ensemble.

Thanks and sorry for the length, probably a residue from the mentioned loop.

francesco pietra

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