Re: [gmx-users] protonation of histidines

On 6/2/16 2:04 PM, Irem Altan wrote: Hi, Thanks. Is there something I can read to get more information as to how this is done? The source code. It's just a hydrogen bond search. If the putative donor and acceptor atoms satisfy the typical distance cutoff (0.35 nm) and angle (>= 150)

Re: [gmx-users] protonation of histidines

Hi, Thanks. Is there something I can read to get more information as to how this is done? Best, Irem > On Jun 2, 2016, at 1:06 PM, Tsjerk Wassenaar wrote: > > Hi Irem, > > pdb2gmx checks the hydrogen bonding network and decides which form of His > fits best. > > Cheers,

Re: [gmx-users] protonation of histidines

Hi Irem, pdb2gmx checks the hydrogen bonding network and decides which form of His fits best. Cheers, Tsjerk On Jun 2, 2016 17:20, "Irem Altan" wrote: > Hi, > > When I process a .pdb structure using pdb2gmx, how does Gromacs add > hydrogens to the histidine residues? I

[gmx-users] protonation of histidines

Hi, When I process a .pdb structure using pdb2gmx, how does Gromacs add hydrogens to the histidine residues? I see that in the processed structure, some histidines have their NE2 atom protonated, while some have ND1 protonated. How does Gromacs decide which nitrogen to protonate? Best, Irem