[gmx-users] Choosing terminals with AMBER ff

[Simon Kit Sang Chu]

Hi everyone,

I am considering selecting specific terminal caps, i.e. neutral N-terminal,
charged C-terminal, with AMBER forcefield. However, there does not seem
such an option.

I ran "gmx pdb2gmx -f protein.pdb -o protein.gro -p protein.top -i
protein.itp -ter -ignh". After selecting AMBER99SB_ILDN and TIP3P, I cannot
choose my terminals. The topology file automatically chooses charged for
both ends.

Is there any way to work around it? I am simulating part of a protein.
Therefore, the N-terminal should not be charged.

Regards,
Simon