Re: [gmx-users] Protonation state of the ionisable residues

James Starlight wrote: Thanks Justin. Your aproach is very usefull indeed. I've just one relative question about CAPPING of the termi in the case of simulation of the membrane receptors. In that proteins both of N and C termi are in the water polar layer. In the literature I've found noth

Re: [gmx-users] Protonation state of the ionisable residues

Thanks Justin. Your aproach is very usefull indeed. I've just one relative question about CAPPING of the termi in the case of simulation of the membrane receptors. In that proteins both of N and C termi are in the water polar layer. In the literature I've found nothing about capping of the termi

Re: [gmx-users] Protonation state of the ionisable residues

James Starlight wrote: Dear Gromacs Users! I'd like to change default protonation state of some specified Glu and Asp residues im my protein. By defaylt pdb2gmx -ignh create unprotonated state of the negatively charged residues but I want to make 2 of such residues protonated to mimick

[gmx-users] Protonation state of the ionisable residues

Dear Gromacs Users! I'd like to change default protonation state of some specified Glu and Asp residues im my protein. By defaylt pdb2gmx -ignh create unprotonated state of the negatively charged residues but I want to make 2 of such residues protonated to mimick some intermollecular interactio