[gmx-users] Add custom residue to DNA index group
william Stebbeds
willstebbeds at hotmail.com
Fri Feb 11 19:44:06 CET 2011
Ok, will do.
Thanks very much
Will
> Date: Fri, 11 Feb 2011 13:29:53 -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:
> > 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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