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

[Mark Abraham]

Hi,

A more considerate approach to asking for others' time is to describe your
actions and output more completely when first asking.

Mark

On Tue, Feb 6, 2018, 05:22 Мижээ Батсайхан <b.mijiddorj at gmail.com> wrote:

> Dear Mark,
>
> Thank you very much for your answer. In the modelled structure, there is no
> missing atoms. Actually, I used -ignh option for pdb2gmx, and it give this
> error. This error releated to the hydrogen atoms in the structure. It give
> me following warning:
>
> WARNING: atom HE3 is missing in residue DTRP 7 in the pdb file
>          You might need to add atom HE3 to the hydrogen database of
> building block DTRP in the file merged.hdb
>
> However, I used pdb2gmx without -ignh option, and  it was no problem.
>
>
> Best regards,
>
> Miji
>
>
>
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 05 Feb 2018 11:46:57 +0000
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] regarding "-missing" option of pdb2gmx
> > Message-ID:
> >         <CAMNuMAQ6S9hHGW0MzFzfhEexsDUkjh2FM5qhAhXijXcJSRp-xA at mail.
> > gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 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 ????? ????????? <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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