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
> _______________________________________________
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> 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
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Received on Thu Jul 08 2010 - 20:30:03 PDT
