> I am going to take your advice and try to write a program to convert the
> gromacs topology to amber's.
Another possibility would be to find papers using amber for
nanotubes, and ask the authors how they did it.
> 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.
See the tutorials that involve creating new ligands to see
how a 'frcmod' file can be used to modify or add custom parameters.
I don't remember reading anything here on parameters conflicting
with implicit solvent, so wouldn't anticipate a problem, but this
isn't the authoritative answer :-)
> I am also will include free ions in the system with implicit solvent. Will
> the free ions be an issue? Thanks.
I never used implicit solvent, not sure.
Bill
> 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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Received on Thu Jul 08 2010 - 17:00:03 PDT
