Re: [gmx-users] Nucleic Acid Simulations with Gromacs

I would also suggest amber force field ports. I managed to run a simulation with Amber ff 99 and TIP3P water model in Gromacs. Good luck, Anna On 10/2/07, Monika Sharma <[EMAIL PROTECTED]> wrote: > Dear All, > I want to start nucleic acid simulations. I am using gromacs3.3.1. But I > could not fi

[gmx-users] producing top and gro files for the molecule with metal ions.

Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ ) has parameters on

Re: [gmx-users] DNA simulations with GROMACS???

Hi! Thank you all very much for the help! The problem was in correct usage of water models. I used amber_tip3p.gro and gromacs_tip3p.itp. So, it is necessary to use both tip3p.gro and tip3p.itp from either amber or gromacs. regards /anna On 6/19/07, Anna Reymer <[EMAIL PROTECTED]> wrot

Re: [gmx-users] grompp or parameter file problem?

On 6/20/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Anna Reymer wrote: > Hello all! > > I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. > I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. > When running grompp: > &

Re: [gmx-users] grompp or parameter file problem?

here if you are not sure about your answers towards above two questions. Regards, Yang Ye - Original Message From: Anna Reymer <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, June 20, 2007 10:57:28 PM Subject: [gmx-users] grompp or parameter file problem? Hello all!

[gmx-users] grompp or parameter file problem?

Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. When running grompp: grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr with the following em.mdp: -

Re: [gmx-users] DNA simulations with GROMACS???

Hi again! The end of my top file looks : [ molecules ] ; Compound#mols Protein 1 SOL 10682 /Anna On 6/19/07, Erik Marklund <[EMAIL PROTECTED]> wrote: 19 jun 2007 kl. 09.31 skrev Anna Reymer: > Dear GROMACS users! > > Is it possible to model DN

[gmx-users] DNA simulations with GROMACS???

Dear GROMACS users! Is it possible to model DNA with the help of GROMACS with AMBER ports? I've checked mailing-list and found that the only GROMCAS force field appropriate for modeling DNA is OPLS, but it does not provide good enough results for long DNA MD runs. The mailing-list suggested AMBER