[gmx-users] Choosing terminals with AMBER ff

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 8 11:36:52 CET 2017


AMBER didn't parameterize things that likely don't exist under biological
conditions. You can build on a proper capping group that is present in
aminoacids.trp, however, such as ACE.


On Wed, Nov 8, 2017 at 7:24 AM Simon Kit Sang Chu <simoncks1994 at gmail.com>

> 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
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