Hi Lin, > 1. Although you have explained the differece between HOH, AHOH and > BHOH, I do not fully understand. => Can I delete all of atoms, > HOH, AHOH and BHOH ?
You can delete one of them, either A or B, if you want to include the water in your model. It may be that pdb2gmx discards the B series in favor of the A one by default, but I'm not sure about that. > 2. So, in your tutorial, you use "united atom" algorithm, right? > and, "pdb2gmx" can recognize the "united atoms" and give them the > proper force fields, right? You mix up a few things. It's the force field that is united atom (or all atom). When running pdb2gmx you choose a force field to use to describe your system. Based on that choice, pdb2gmx will convert your structure in the proper way, adding all hydrogen atoms that need to be included according to the force field. > 3. If one want to use the "all-atom algorithm", use the command > "protonate + protein pdb file" first to add all missing hydrogens, > then, use "pdb2gmx" to get an all-atom force field parameters, right? David answered this one. > 4. In your last email => where did you get the following information? > => I re-check the original 1LW9.pdb => I did not get the information by > myself. It's in the file format specification, not in the file. See http://www.wwpdb.org/docs.html > "The answer to this question is in the format specification of the PDB > file. The A and B are alternative identifiers and indicate that the > electron density can be explained by a water molecule that is > partially present at two sites. If you look at the occupancy field > you'll notice that the corresponding values are less than 1. In fact, > if you sum the occupancies for equivalent atoms in for A and B, they > will add up to 1." > Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
