[gmx-users] regarding "-missing" option of pdb2gmx

[Mark Abraham]

Hi,

You're modelling a physical system, so you have to know what you intend to
model. What atoms are missing? Is that consistent? Why would you even
consider running with a topology that is inconsistent with your intent?

Mark

On Mon, Feb 5, 2018, 07:58 Мижээ Батсайхан <b.mijiddorj at gmail.com> wrote:

> Dear gmx users,
>
> I want to perform MD simulations of D-amino acid containing protein, and
> force field is charmm36, last version, which contains the parameters of
> D-amino acids. When I use pdb2gmx, I received following error:
>
> Fatal error:
> There were 10 missing atoms in molecule Protein, if you want to use this
> incomplete topology anyhow, use the option -missing
>
> My questions:
> 1. Can I use above -missing option for pdb2gmx?
> 2. What is the effect in the results in case of using the incomplete
> topology?
>
> Best regards,
>
> Miji
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