Thanks Jason.
Yes I also feel that would be tricky. But The carbon nanotube has quite
tricky structure that if you break a tube into two for topology purpose
(with antechamber), when putting their topology together, I feel that I need
to manually add a lot of bond/angles/dihydrals. And I may need to use
different sized nanotubes.
As for why I changed from gromacs to amber. I want to simulate ~ 15k atoms
containing nanotubes and polymers. It may take gromacs >100 years for 1 ns
with explicit water.
And I was told that amber has the best implicit solvent simulation ability.
BTW. It seems that gromacs has coarse-grain ability but no implicit solvent,
while amber has implicit solvent but no coarse-grain.
Yan
On Thu, Jul 8, 2010 at 8:26 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jul 8, 2010 at 7:26 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
>
> > Thanks Bill.
> >
> > I am going to take your advice and try to write a program to convert the
> > gromacs topology to amber's.
> >
>
> This could be quite tricky. In order to do this, you'll have to understand
> both types of topology files as well as how to convert one into the other.
> Understanding the Amber topology file itself is very difficult. You'd
> probably be better off using pre-established programs to create your
> topology file(s).
>
> I have another question regarding the force field.
> > I use customized FF in gromacs, so I would wish to keep it customized in
> > amber. May I know if it is doable? And if a customized FF will physically
> > conflicted with the implicit solvent which I want to apply? (Or if the
> > result be un-trustable ) Thanks.
> >
>
> Why are you trying to switch to Amber? Is there something you can do with
> Amber that you can't with gromacs?
>
>
> Good luck!
> Jason
>
>
> > I am also will include free ions in the system with implicit solvent.
> Will
> > the free ions be an issue? Thanks.
> >
> > Regards,
> > Yan
> >
> > On Thu, Jul 8, 2010 at 2:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > > I want to simulate carbon nanotubes (CNT) with implicit water, so I
> > need
> > > to
> > > > translate the topology from Gromacs format to Amber format.
> > >
> > > > I tried antechamber using the pdb file, planning to manually modify
> the
> > > > parameters after the file is constructed. However my tube is big
> (1200
> > > > carbon atoms), and antechamber said "The atom number exceeds the
> > MAXATOM,
> > > > reallocate memory", and eventually crashed.
> > >
> > > > I also think of divide the long tube into small ones, but it seems
> that
> > I
> > > > need to manually add the bond/angle/dihydral to connect the small
> > tubes.
> > > The
> > > > number of connections seems to be quite large, and I am not quite
> know
> > of
> > > > how to add it. So I still look for a better way of doing it.
> > >
> > > You will need bond, angle and dihedral parameters whether the
> > > molecule is one residue or many. But specifying the many
> > > connections between multiple smaller residues could be a chore.
> > > You might want to write a program to generate the leap cmds
> > > to do this. It might also be tricky to turn a 1-residue pdb
> > > into a multi-residue pdb; if the 1-res pdb was generated by
> > > a program, you may want to modify that program.
> > >
> > > Given all that, it may be worth trying to debug antechamber
> > > to allow the 1-res version.
> > >
> > > Bill
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Yan Gao
> > Jacobs School of Engineering
> > University of California, San Diego
> > Tel: 858-952-2308
> > Email: Yan.Gao.2001.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Thu Jul 08 2010 - 22:00:04 PDT
