Richard Mariadasse

6 Questions 10 Answers 0 Followers

Questions related from Richard Mariadasse

Getting error when performing DNA dynamics in Gromacs?

I wish to perform MDS to DNA molecule for 100 ns time using Gromacs software. Until energy minimization step, i did not get any error. But when i perform NVT step, the error appeared like "Group...

08 August 2016 3,458 3 View

Protein-Peptide docking

I am facing problems while running the peptide docking. First I tried using the peptide docking panel provided by the BioLuminate module since there is a provision in providing the peptides in the...

07 July 2014 7,283 7 View

Can someone suggest an analysis to perform a membrane protein simulation?

I am running a 30 ns membrane protein simulation in Desmond using DPPC as the lipid bilayer. What sort of analysis can be performed?

06 June 2014 2,143 6 View

Can anyone help with a membrane protein simulation problem?

While am running the EM, the minimizatin gets stopped before the forces get converged at step 14 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step=...

05 May 2014 9,944 1 View

Can someone explain an error I encountered when running membrane protein simulation following the tutorial mentioned below?

After converting the dppc128.pdb to gro format the next step is generating the em.tpr file using grompp but I constantly get this error: atomtype OW not found Can anyone please suggest where...

05 May 2014 7,937 2 View

Membrane protein simulation problem - Can anyone help?

I updated the toplogy file. After that I used this command grompp_mpi -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr ERROR 5877 [file topol.top, line 13629]: No default LJ-14...

05 May 2014 1,466 2 View