Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions

From: Yan Gao <>
Date: Thu, 8 Jul 2010 16:26:55 -0700

Thanks Bill.

I am going to take your advice and try to write a program to convert the
gromacs topology to amber'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.

I am also will include free ions in the system with implicit solvent. Will
the free ions be an issue? Thanks.


On Thu, Jul 8, 2010 at 2:28 PM, Bill Ross <> 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

Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
AMBER mailing list
Received on Thu Jul 08 2010 - 16:30:03 PDT
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