Thank you Bill.
That's a good idea. Actually I am still not fully understand the topology
structure in amber, and feel that it may take me quite some time. So I used
a "try".
Regards,
Yan
On Thu, Jul 8, 2010 at 4:46 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> 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 - 22:00:03 PDT
