Hi, > No, that procedure generates a topology file, it is not the correct tool for > a change of coordinate format (which is almost never needed anyway). As a > side effect, it regularizes an input coordinate file which might have been > in one of various formats, and outputs a coordinate file whose default > format happens to be .gro (but could be a range of possibilities). I wish > tutorial writers would not give new people the wrong impression about the > purpose of this step! >
>From my tutorial (http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html): Structure conversion and topology A molecule is defined by the coordinates of the atoms as well as by a description of the bonded and nonbonded interactions. Since the structure obtained from the PDB only contains coordinates, we first have to construct the topology, which describes the system in terms of atom types, charges, bonds, etc. This topology is specific to a certain force field and the force field to be used is one of the issues requiring careful consideration. Here we use the GROMOS96 53a6 united atom force field, which is parameterized to give good predictions of free energies of solvation of amino acid side chains and which generally gives good agreement with NMR experiments. It is important that the topology matches with the structure, which means that the structure needs to be converted too, to adhere to the force field used. To convert the structure and construct the topology, the program pdb2gmx can be used. This program is designed to build topologies for molecules consisting of distinct building blocks, such as amino acids. It uses a library of building blocks for the conversion and will fail to recognize molecules or residues not present in the library. Issue the following command to convert the structure; choose the GROMOS 53a6 force field when prompted. Note the flag -ignh, which causes hydrogen atoms present in the file to be removed, and to be rebuild according to the description in the force field. pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh Read through the output on the screen and check the choices made for the histidine protonation and the resulting total charge of the protein. Also browse through the input structure file (protein.pdb, pdb format) and output structure file (protein.gro, gromacs format). Note the differences between the two formats. Also note that the output structure file could as well have been chosen to be in pdb format. Now browse through the topology file and look at the structure. Write down the number of atoms before and after the conversion and explain the difference List the atoms, atom types and charges from a tyrosine residue as given in the topology file ### TAW -- 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 [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
