Re: [gmx-users] partial charge on protein

Homa Azizian wrote: Hi Justin and all when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce with OPLS force field. it seems that the protein has the charge of -3, while the ligand has the charge of 0.890 and finally it prints that the final charge is -2.11. I neutralized this charg

Re: [gmx-users] partial charge on protein

Homa Azizian wrote: Hi according to my problem about non-neglible magnitude partial charge on protein, I did not use -missing option with pdb2gmx my command is: pdb2gmx -ignh -f .pdb -o .pdb -water spce what should I do to neutralize this charge? You should probably start over and check car

Re: [gmx-users] partial charge on protein

Homa Azizian wrote: Hi there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or it should better ignore this? You should absolutely NOT ignore this problem. You have a fractional charge of non-negligible magnitude. Did you use -missing with pdb2gmx? If so, you are pro