[gmx-users] change angle type in ffbonded.itp

hello I'm using Gromacs with charm27.ff force-field.I adding a new residue (NAG) in force field I have a problem with water molecules in my system: During minimization, I have this message: step X: Water molecule starting at atom XXX can not be settled. Check for bad contacts and/or reduce the

[gmx-users] i have a question about multiple chain simulation at the same box

I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box

[gmx-users] A question about Protein-Protein Docking with Gromacs

In many cellular signaling pathways in cancer cells, the expression of many genes rises. One result of this excessive expression is cellular traffic and unwanted interactions between proteins. Therefore, it is important to examine the interactions and identify the amino acids involved in the

[gmx-users] i have queston about partial charge zinc

Hi I gonna MD simulation a protein that contained a zinc ion for build topology I used from the amber99sb force field Atomic charge is written "+2" in topology. I wanted to ask if this charge is correct or should be calculated in a different way? "PDB id 4row" sincerely -- Gromacs Users mailing

[gmx-users] A question about Protein-Protein interaction with Gromacs

In many cellular signaling pathways in cancer cells, the expression of many genes rises. One result of this excessive expression is cellular traffic and unwanted interactions between proteins. Therefore, it is important to examine the interactions and identify the amino acids involved in the

[gmx-users] Side chains protein interaction: determine the type of interaction of two amino acids at the atomic level

Dear researcher I want to check the effect of an SNP (Single-nucleotide polymorphism) in my protein structure. To do this, I once simulated a protein in the Wild Type state and once again mutated for 100 nanoseconds. After performing the MD, The defect of many articles I have read in

[gmx-users] how to calculated potential energy ?

Dear researcher I want to measure the following parameters for a part of a protein Intramolecular potential energy protein surface potential Ebond, bond length potential energy contribution Eangle, bond angle potential energy contribution Etorsion, torsion angle potential energy contribution

[gmx-users] how we can add these ions depends on precise physiological concentration?

Dear researcher As we know, we add only specific ions including Na and Cl to simulation box for conducting molecular dynamics simulation. The question is raised is why we don't add other ions to simulation box that are existed in the cell environment, for example, phosphate or potassium? It is

[gmx-users] Please explain why this article has been accepted

Please explain why this article has been accepted Please refer to the RMSD chart https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064364 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] calculate potential energy or short-range and long-range energy and enthalpy per residue

I performed MD for apoprotein after this I want to calculate potential energy or short-range and long-range energy and enthalpy "per residue" please help me how can I do this? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] how to calculate potential energy or short-range and long-range energy and enthalpy per residue

I performed MD for apoprotein after this I want to calculate potential energy or short-range and long-range energy and enthalpy "per residue" please help me how can I do this? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] calculate potential energy or short-range and long-range energy and enthalpy per residue

I performed MD for apoprotein after this I want to calculate potential energy or short-range and long-range energy and enthalpy "per residue" please help me how can I do this? -- Gromacs Users mailing list * Please search the archive at