[gmx-users] :a grompp problem using a ffamber port

David Mobley dmobley at gmail.com
Wed Oct 26 19:54:55 CEST 2005


You might want to correspond with the Pande group on this, as they're the
ones who put out the port.

I had a similar problem with Cl- ions and, as a temporary solution, modified
the ions.itp file in the top directory to have an #ifdef _FF_AMBER section
specifying the appropriate ion definitions (copied from earlier in the
ions.itp file but changing the atom types to the amber atom types -- i.e.
CL- is amber94_30). My conclusion was that no ion parameters were being
loaded when _FF_AMBER was defined, so I thought this was necessary. I
remember corresponding with Eric Sorin (Pande group) on this and he had some
alternative method of setting up systems where this wasn't a problem, I

Anyway, you'll probably need to talk to them, as the Amber FF is not a part
of Gromacs, so in general you probably won't get support from this list.


On 10/26/05, sara pistolesi <sarapistolesi at hotmail.com> wrote:
> Dear alll,
> I'm trying to carry out a MD simulation on a small RNA molecule. Then I've
> downloaded the ffamber99 force field port for gromacs ,modified my pdb file
> and runed pdb2gmx. I've solvated the system using ffamber_tip4p files and
> neutralized the system charge using Na+ ions.
> But when I run grompp command for energy minimization the software is not
> able to recognize Na+ ions (I tryed to write it in all possible ways, NA+,
> NA, Na+ and Na, but the results are the same).
> How may I do?
> Thanks in advance.
> Bests,
> Sara Pistolesi
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