[gmx-users] Add custom residue to DNA index group
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 11 19:29:53 CET 2011
william Stebbeds wrote:
> I made the changes to ../gromacs/top/residuetypes.dat
>
> the Make_ndx output:
>
> 0 System : 34023 atoms
> 1 DNA : 650 atoms
> 2 DGO : 66 atoms
> 3 K : 43 atoms
> 4 CL : 21 atoms
> 5 Other : 66 atoms
> 6 DGO : 66 atoms
> 7 K : 43 atoms
> 8 CL : 21 atoms
> 9 Ion : 64 atoms
> 10 DGO : 66 atoms
> 11 K : 43 atoms
> 12 CL : 21 atoms
> 13 Water : 33243 atoms
> 14 SOL : 33243 atoms
> 15 non-Water : 780 atoms
> 16 Water_and_ions : 33307 atoms
>
> This system consists of a 22 residue DNA molecule, two of which are DGO,
> each have 33 atoms.
>
> I also do not understand why DGO is repeated three times.
>
There have been significant changes to the generation of default groups for
indexing since the 4.0.x series. I would suggest you upload your input files
and a description of the problem to the Redmine system so it can be investigated
and fixed. I've seen the same issue with duplicate moleculetypes, which looks
like it's happening for several species here. It's definitely something worth
fixing.
http://redmine.gromacs.org/
For now, you can just merge DNA and DGO and create a complete index group.
-Justin
> Thanks again
>
> will
>
>
> > Date: Fri, 11 Feb 2011 12:08:52 -0500
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Add custom residue to DNA index group
> >
> >
> >
> > william Stebbeds wrote:
> > > Indeed I did
> > >
> > > DGO DNA
> > >
> >
> > Did you make the change system-wide, or in a local directory? If the
> latter,
> > you have to issue all your commands in that same directory or else
> the default
> > residuetypes.dat (in GMXLIB) will be read.
> >
> > Can you post the make_ndx output (i.e. list of groups)?
> >
> > -Justin
> >
> > > Cheers
> > >
> > > Will
> > >
> > > > Date: Fri, 11 Feb 2011 17:57:32 +0100
> > > > Subject: RE: [gmx-users] Add custom residue to DNA index group
> > > > From: dsarath at gwdg.de
> > > > To: gmx-users at gromacs.org
> > > >
> > > > >
> > > > > Thanks for the quick reply,
> > > > >
> > > > > I have already done that, and GROMACS, in all other cases,
> knows it is
> > > > > DNA, as it automatically forms the bonds with other residues.
> > > > >
> > > > > it is only when it makes its index files that it doesnt know
> that my
> > > > > residue is DNA.
> > > > >
> > > >
> > > > Did you make the change in residuetypes.dat file.
> > > > add your residues XXX as DNA in the residuetypes.dat file
> > > >
> > > > eq: XXX DNA
> > > >
> > > >
> > > >
> > > > Best Wishes,
> > > >
> > > > Sarath
> > > > > Cheers
> > > > >
> > > > > Will
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Date: Sat, 12 Feb 2011 03:33:15 +1100
> > > > > From: Mark.Abraham at anu.edu.au
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: Re: [gmx-users] Add custom residue to DNA index group
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Message body
> > > > >
> > > > >
> > > > > On 12/02/2011 3:14 AM, william Stebbeds wrote:
> > > > >
> > > > >
> > > > > Hi Folks,
> > > > >
> > > > >
> > > > >
> > > > > I have added a custom DNA residue to the amber99sb ff, and
> > > > > everything works perfectly, (thanks to Justin!).
> > > > >
> > > > >
> > > > >
> > > > > The residue is incorporated perfectly into the sequence, with no
> > > > > abnormal events during simulations. I have updated all the files
> > > > > to include the new residue.
> > > > >
> > > > >
> > > > >
> > > > > I have since realised, when using g_rms, that my custom residue is
> > > > > not included in the default DNA index group, and appears as a
> > > > > group on its own.
> > > > >
> > > > >
> > > > >
> > > > > Is there a way of making gromacs understand that this residue is
> > > > > DNA when it makes the index files?
> > > > >
> > > > >
> > > > >
> > > > > I am not using make_ndx, I just let gromacs split the groups.
> > > > >
> > > > >
> > > > >
> > > > > Thanks in advance
> > > > >
> > > > >
> > > > >
> > > > > Will - Cranfield University
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > You need to arrange for the tools to access a modified form of
> > > > > share/gromacs/top/residuetypes.dat with your custom residue
> suitably
> > > > > classified. I understand you can copy that file to your working
> > > > > directory and modify it there, and GROMACS will use the local copy.
> > > > >
> > > > >
> > > > >
> > > > > Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
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> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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