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

gt; > Message: 3 > > Date: Mon, 05 Feb 2018 11:46:57 + > > From: Mark Abraham <mark.j.abra...@gmail.com> > > To: gmx-us...@gromacs.org > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] regarding "-missing" option of pd

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

Mon, 05 Feb 2018 11:46:57 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] regarding "-missing" option of pdb2gmx > Message-ID: > <CAMNuMA

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

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

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

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