rmat.
>
> *http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder
>
> HTH
>
> Stéphane
>
> --
>
> Message: 3
> Date: Tue, 24 Oct 2017 17:17:08 +0200
> From: Elisa Pieri
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Conv
ware/software/ACPYPE-folder
HTH
Stéphane
--
Message: 3
Date: Tue, 24 Oct 2017 17:17:08 +0200
From: Elisa Pieri
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID:
Content-Type: text/plain; charset="UTF-8"
Hel
Hello again,
Thank you very much for your answers, we got to convert everything. We used
pdb2gmx with no problems, and the conf.gro file looks fine (on VMD at
least). Then, we tried with a simple input file (from
http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf), but grompp
reports a f
On Mon, Oct 23, 2017 at 11:10 AM Elisa Pieri
wrote:
> Hello again,
>
> sorry I wasn't very clear perhaps..we are trying to modify directly the
> ffbonded.itp file (together with all the other interested ones) in the
> Amber94 force field in order to include the Amber Lipids17 force field. We
> ad
Hi,
The multiplicity/periodicity is the same but always positive in GROMACS.
Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by
IDIVF (the entry after names in AMBER file). The phase is the same.
For more info on why see ambermd.org/formats.html#parm.dat
Cheers
Tom
On 23/
Hello again,
sorry I wasn't very clear perhaps..we are trying to modify directly the
ffbonded.itp file (together with all the other interested ones) in the
Amber94 force field in order to include the Amber Lipids17 force field. We
added most of the parameters with no problems (bond equilibrium len
ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
appropriate software for converting topologies.
This is the parm.py script I have employed, supply amber topologies
file.prmtop and file.inpcrd as input and amber.save option will give
converted gromacs topologies as output.
i
You can do with ParmEd
On Oct 20, 2017 10:07 PM, "Elisa Pieri" wrote:
> Hello GMX users/developers,
>
> we are trying to add the Amber lipids17 forcefield to the Amber99
> forcefield implemented in Gromacs. We are a little bit lost on the torsion
> parameters: how to convert the constant from Amb
Hello GMX users/developers,
we are trying to add the Amber lipids17 forcefield to the Amber99
forcefield implemented in Gromacs. We are a little bit lost on the torsion
parameters: how to convert the constant from Amber to Gromacs?
Thank you in advance!
Elisa
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