Re: [gmx-users] make_ndx option

[Rubben Torella]

Hi Anirban,
when you choose in make_ndx, you choose group 3 and (&) r 2 3 4 5 6...and so
on...
in make_ndx there is a legend that explain this passage well...
Bye!

2009/7/9 Anirban Ghosh 

> Hi ALL,
>
> I want to create an index file using make_ndx which will contain only
> C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res
> 36-40). How should I give this option in make_ndx. Any suggestion is
> welcome.
>
> Regards,
>
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
> --
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Re: [gmx-users] Re: Problem with AMBER-GROMACS DNA database residue

[Rubben Torella]

Hi, Alan
Thank you very much for your quick answer.
You understand well my problem...
I normally use amb2gmx for proteins, and, changing some residue names (ex.
CYM-->CYS..), it works correctly...
It's the first time that I work with DNA, and I have this problem...
thank you for your help
Rubben

2009/7/1 Alan 

> Hi there,
>
> Not really clear what you did or want to do, so I'll do assumptions.
>
> If your have you prmtop and inpcrd files working fine with AMBER (sand
> or pmemd) then you just want to run this with GMX (mdrun ...).
>
> So, you can try amb2gmx.pl program or (better), look at
> acpypi.googlecode.com, and you can find how to use 'acpypi' for
> converting amber topology files to gromacs topol files.
>
> Cheers,
> Alan
>
> On Wed, Jul 1, 2009 at 10:25,  wrote:
> >
> > Hi, gmx-users,  I have a problem to "translate" nitrogen base residue
> names
> > from AMBER to GROMACS.
> > I have simulated with AMBER a DNA-protein complex, then i have changed in
> > the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA,
> > DC-->DCYT, DA-->DADE, in order to "translate" the MDs from AMBER to
> > GROMACS... but in the prmtop file are present also DT5, CT3, that
> indicate
> > the residues at the end of the chains... anyone knows which is the
> correct
> > GROMACS residue name for these residues? I have searched in the ff.rtp
> file
> > but seem that these particular residues are not present...
> > Thank you in advance...
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
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[gmx-users] Problem with AMBER-GROMACS DNA database residue

[Rubben Torella]

Hi, gmx-users,  I have a problem to "translate" nitrogen base residue names
from AMBER to GROMACS.
I have simulated with AMBER a DNA-protein complex, then i have changed in
the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA,
DC-->DCYT, DA-->DADE, in order to "translate" the MDs from AMBER to
GROMACS... but in the prmtop file are present also DT5, CT3, that indicate
the residues at the end of the chains... anyone knows which is the correct
GROMACS residue name for these residues? I have searched in the ff.rtp file
but seem that these particular residues are not present...
Thank you in advance...
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