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

[Мижээ Батсайхан]

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>