Re: [gmx-users] problem in defining protonation state of amino acids

Hi Justin, Thanks for your valuable suggestion. I ignored the hydrogen and added manually bu -his flag. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] problem in defining protonation state of amino acids

Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I calculated protonation state of various amino acid at required pH using H++ server. However when trying to run pdb2gmx got fatal error Atom HB3 in residue SER 3 was not found in rtp entry SER with 11 atoms while

Re: [gmx-users] problem in defining protonation state of amino acids

On 3/13/15 8:08 AM, Tushar Ranjan Moharana wrote: Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I Just for clarity fixed protonation and constant pH are not synonymous. Natively, GROMACS does not do constant pH simulations, though I believe some groups