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= 0.000 +/-0.000 kJ/mol WCA energy = 0.000 +/-0.000 kJ/mol Binding energy = nan +/- nan kJ/mol === END === *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics

[gmx-users] (no subject)

...? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

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with: ' '... Kindly need your valuable suggestions in this regard. With regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- *Saranya Vasudevan

[gmx-users] (no subject)

from the protein. I have applied pBC and sure this is not an visualisatuin error. How can I rectify this, Kindly give your valuable suggestions in this regard. -- *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University

[gmx-users] (no subject)

--- Anyone can help me in overcoming this fatal error will be appreciated. With Regards, Saranya Vasudevan, Research Scholar, Molecular Quantum Mechanics Laboratory, Department of Physics, Bharathiar University, Coimbatore-46 -- Gromacs Users mailing list * Please

[gmx-users] (no subject)

instead of 4 peptide structure i got only a single peptide structure. What is the reason for getting this result? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs

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over protein increase/decrease with a number of hydrogen bonds? Or even a single bond between protein and ligand is more sufficient to bring necessary changes to a protein? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics

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Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. The number of H-bond formation is very low I have a question about is there any influence of the drug in my protein? With Regards, *Saranya

Re: [gmx-users] (no subject)

There is a minimum number of hydrogen bond formation (2 hydrogen bonds) in my protein-drug complex. I have a question about is there any influence of the drug in my protein-drug complex. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

drug interaction? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] (no subject)

drug interaction? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] Gromacs

after NVT *With Regards,* *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] (no subject)

Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46

[gmx-users] (no subject)

Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46

[gmx-users] (no subject)

Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46

Re: [gmx-users] Gromacs

i tried to run in OPLSAA force field sir. *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* On Tue, Oct 6, 2015 at 7:39 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > Maybe y

[gmx-users] (no subject)

to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? *With Regards,* *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs

Re: [gmx-users] Gromacs

to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? With Regards *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs