Hi Rebeca,
I guess you're confusing things here because there's no SPC water in Amber,
but there's SPCE. Besides (although I don't remember the reference, but
google and lists are your friend), SPCE water is the best water model AFAIK.
And if you allow me a suggestion, why don't you try acpypi instead of
amb2gmx.pl?
You may find some reasons for that here:
http://code.google.com/p/acpypi/wiki/HowAcpypiWorks
I hope it can helps.
Alan
On Wed, Jun 3, 2009 at 15:46, rebeca <rebeca.mmb.pcb.ub.es> wrote:
> Hi,
> I am trying to simulate a system using the parameters for ions developed by
> Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
> I have the topology and the crd file. Now, I want to obtain the topology
> for Gromacs using amb2gmx.pl, so I must change the default parameters (for
> tip3p) included in amb2gmx.pl.
> I have seen that in the .tar file ffamber_v4.0 there is no a corresponding
> itp file for spc model of water in amber, so what parameters should I
> include for the section of bondtypes, angletypes, atoms, bonds, angles,
> settles,...? Those corresponding to the SCP in Gromacs directly?
> Thank you very much for your help.
> Best wishes,
>
>
> --
> Rebeca García Fandiño
> Molecular Modelling and Bioinformatics Group
> Institut de Reçerca Biomèdica
> Parc Cientific de Barcelona
> 08028 Barcelona
> rebeca.mmb.pcb.ub.es
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Thu Jun 04 2009 - 01:10:21 PDT
