[gmx-users] regarding "-missing" option of pdb2gmx
b.mijiddorj at gmail.com
Tue Feb 6 05:22:29 CET 2018
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.
> 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
> <CAMNuMAQ6S9hHGW0MzFzfhEexsDUkjh2FM5qhAhXijXcJSRp-xA at mail.
> Content-Type: text/plain; charset="UTF-8"
> 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?
> 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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