Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges using UCSF chimera. I
thereafter use acpype to get the ligand's gro,itp and top files. Finally, i
process the protein.PDB file and perform MD simulations. However, when
Dear users
I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
How can I know in which FF these are present?
And what can I do if no FF include the interested Ions?
any suggestion is appreciated in advacne
Best
Mohsen
--
gmx-users mailing listgmx-users@gromacs.org
Have you tested your ligand alone in MD simulation and how vmd would show
it?
Alan
On 21 October 2013 08:31, MUSYOKA THOMMAS mutemibiochemis...@gmail.comwrote:
Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
Dear users
I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
How can I know in which FF these are present?
Phosphorus and sulfur aren't ions. There are P and S atomtypes in most force
fields that are suitable for several
Sounds like issues with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
strategies for coping found there.
Mark
On Mon, Oct 21, 2013 at 9:31 AM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Users,
I am doing protein-ligand MD simulations. I first
Please keep the discussion on the gmx-users mailing list.
On 10/21/13 6:24 AM, sunyeping wrote:
Dear professor Lemkul,
Thank you for the reply. But I still have some questions about the umbrella
sampling tutorial. In setion 2 of the tutorial, define the unit cell, for the
command:
editconf
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in my solution.
On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
Dear
On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in my solution.
Many force fields include these ions or closely related model compounds. Have a
sure, thank you.
On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
equilibration by GROMACS. I know GROMACS can build the system, but my
subsequent production run must be conducted by CHARMM. I want to use
GROMACS to do equilibration cuz it may take long to get it equilibrated.
On 10/21/13 11:14 AM, Zhi Yue wrote:
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
equilibration by GROMACS. I know GROMACS can build the system, but my
subsequent production run must be conducted by CHARMM. I want to use
GROMACS to do equilibration cuz
Hi Justin,
Thanks for your advice. I'll try again. Have a wonderful night!
Best
Shane
On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 11:14 AM, Zhi Yue wrote:
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
I have completed the simulations using couple-intramol = yes
Reminder, have a molecule that are calculating the Gibbs energy of hydration
and solvation (octanol). In one topology the only difference is the atomic
charges have been doubled. Considering that charges are scaled linearly with
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