On 2012-04-06 06:41:57PM -0700, Acoot Brett wrote: > Dear All, > > Can I remove all the H from the PDB file and then input it to the pdb2gmx so > that pdb2gmx can produce all the correct protonation state of the protein > residues including HIS? > > Cheers, > > Acoot
It will not do what you expect. There is no "magical way" for pdb2gmx to determine HIS protonation. The best it can do is calculate potential H-bonding and assign protons from there; and there is no guarantee it will be "correct" or fit your expectations. You should really determine what criteria to choose for histidine protonation state and assign them manually for best effect. Justin already answered this question in a different way. Perhaps there is a language barrier/problem involved? -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
