[gmx-users] Choosing terminals with AMBER ff

[Simon Kit Sang Chu]

Dear Mark,

Thank you very much. I am worried with the ends attracting each other for a
long peptide. May I ask for the general strategy simulating segments of a
protein? I believe simulating part of the whole protein might not be
something new.

Regards,
Simon

2017/11/8 6:37 下午 於 "Mark Abraham" <mark.j.abraham at gmail.com> 寫道：

Hi,

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.

Mark

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

> 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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