Dear Gromacs Users
I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule
type. (I am using Gromacs, 4.0.5)
It was about Cl and Na. I noticed that because I have selected OPLS forcefield,
I should change the name of Cl and Na in my .top file to Na+ and Cl-.
I did this and
Many thanks for your response. No special reasons for parametrizing the
ligand and the protein as a separate system. I dont think that the ligand
and protein can be parametrized as a single system, but will definitely try
doing it as a single system and see if it works.
Regards
Vijayan.R
On Sat,
Is there a particular reason why the ligand has been parameterized as a
separate moleculetype from the protein in your case? I prefer to treat
coordination bonds as "real bonds" instead of relying on electrostatic
interactions anyway, since it is the only way to conservatively ensure the
coordinati
Dear Gromacs users
I was wondering if there exists any technique that sets
distance restraint between specified ligand (atoms) and the protein(atoms)
in Gromacs. I am simulating a system which contains metal ions coordinated
to the Ligand. I looked in to the mailing list and Gromacs manual and
fi
Hi All,
Does anyone know of a free cheminformatic service from which it's possible
to narrow down a search for molecules by inputting limits on their
molecular parameters, such as molecular weight or the number of hydrogen
bond donors, etc? Such a resource would be of great help.
Thanks in advan
Justin A. Lemkul wrote
>
>
> You don't need the pull code if the two atoms are in the same
> [moleculetype] - a
> "molecule" in Gromacs is any set of atoms; they don't necessarily have to
> make
> chemical sense. The only problem I see is that if you have two atoms in
> the
> same location,
On 5/19/12 5:42 PM, jrustad wrote:
Justin A. Lemkul wrote
I don't know how complex the system is you're dealing with, but at this
point,
isn't it just far more straightforward to construct a rudimentary force
field
with a few atom types rather than rely on (slow) tabulated functions and
pote
Justin A. Lemkul wrote
>
> I don't know how complex the system is you're dealing with, but at this
> point,
> isn't it just far more straightforward to construct a rudimentary force
> field
> with a few atom types rather than rely on (slow) tabulated functions and
> potential funny business to
On 5/19/12 1:13 PM, jrustad wrote:
Thanks- yes, I suspected this might be the case, however, in the context of a
free energy calculation it seems difficult to associate the lookup table
with a molecule type rather than an atom type. In other words, I have
defined a molecule "Fe" which will cha
I thank you all so much for aiding me on this matter, Jan, Peter and Justin.
Now things are way clerarer!
Cheers,
Ricardo.
>
> De: Peter C. Lai
>Para: jalem...@vt.edu; Discussion list for GROMACS users
>
>Enviadas: Sábado, 19 de Maio de 2012 1:01
>Assunto:
Thanks- yes, I suspected this might be the case, however, in the context of a
free energy calculation it seems difficult to associate the lookup table
with a molecule type rather than an atom type. In other words, I have
defined a molecule "Fe" which will change from Fe2 to Fe3.
So, its true th
On 5/19/12 9:06 AM, rama david wrote:
Thank you Justin..
I am sorry Because I am going to ask you the stupid questions but very imp to
me ...
1. Consider your Tutorial In that Instead of using vanderwall radii adjustment
to add water ,
I wish to use keepbyz.sh script ...
In th
Thank you Justin..
I am sorry Because I am going to ask you the stupid questions but very imp
to me ...
1. Consider your Tutorial In that Instead of using vanderwall radii
adjustment to add water ,
I wish to use keepbyz.sh script ...
In these case What would be the value of Lower and
On 5/19/12 8:23 AM, rama david wrote:
Thank you Justin ..
..
I goes through these link ..
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
Please Can any one clearly define me What is Lower Z and Upper Z in the||
keepbyz.sh
Can keepbyz.sh use to remove the water in hydrophob
Thank you Justin ..
..
I goes through these link ..
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
Please Can any one clearly define me What is Lower Z and Upper Z in the
keepbyz.sh
Can keepbyz.sh use to remove the water in hydrophobic region without
affecting
the box dimensio
On 5/19/12 7:49 AM, rama david wrote:
Hi Gromacs friends ..
I am doing justin Lipid-tutoria on lipid ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
I completed upto the ion addition and energy minimisation..
While doing equilibrati
On 5/19/12 6:15 AM, Anirban wrote:
On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak mailto:turgaycakma...@gmail.com>> wrote:
Hi Gromacs users,
I have a question related to the extension of the simulation.
I have done 10 ns simulation (several peptides in a box). Now, I want to
Hi Gromacs friends ..
I am doing justin Lipid-tutoria on lipid ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
I completed upto the ion addition and energy minimisation..
While doing equilibration I stuck with the following problem ..
1
On Fri, 2012-05-18 at 09:49 -0700, Milinda Samaraweera wrote:
> Hi Guys
>
>
> Could you please explain to me how to use the g_dipole method to
> calculate the dipole moment of a Solute in a solvent.
>
Hi,
there has just recently been a discussion on this mailing list. Actually
you need just a
On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak wrote:
>
> Hi Gromacs users,
>
>
> I have a question related to the extension of the simulation.
>
> I have done 10 ns simulation (several peptides in a box). Now, I want to
> extend it 10ns more.
>
>
>
>- As far as I see from “Justin Lemkul’s Lys
Hi Gromacs users,
I have a question related to the extension of the simulation.
I have done 10 ns simulation (several peptides in a box). Now, I want to
extend it 10ns more.
- As far as I see from “Justin Lemkul’s Lysozyme in water tutorial”, to
extend simulation, following should be do
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