Hi: 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 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
