Re: [gmx-users] Fatal error: Protein_A

[EMAIL PROTECTED] wrote: Dear Users, launching the MD I get this fatal error: Fatal error: No such moleculetype Protein_A What does it mean? thanks, Giacomo Bastianelli please go back to the tutorial. this is not an error message you get from mdrun. -- David.

[gmx-users] Fatal error: Protein_A

Dear Users, launching the MD I get this fatal error: Fatal error: No such moleculetype Protein_A What does it mean? thanks, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] Fatal error: Protein_A

Dear Users, launching the MD I get this fatal error: Fatal error: No such moleculetype Protein_A What does it mean? thanks, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] protein constrained, ligand ot constrained

hi Luca, I dont quite understand your point. The benefit of constraints is that they allow you to use a larger timestep of, say, 2 fs instead of 1 fs or so. But if you dont constrain your ligand, you have to use a small timestep anyway, so there is no reason to constrain the protein then. BTW: acco

[gmx-users] Re: conserved quantity

I have now programmed in the conserved quantity (not committed yet). SPC water gives the same energy conservation in NVT Nose-Hoover as in NVE. I did a run of 100 ps for 216 SPC with dt=0.002 ps and SETTLE at 300 K, tau_t=2 ps: NVE: drift per degree of freedom -0.026 kJ/mol /ns NVT: drift per degr

[gmx-users] protein constrained, ligand ot constrained

Dear all, I would like to set up a simulation of a protein-ligand system with the protein left bond-constrained using LINCS algorithm and the ligand left unconstrained, i.e. in order to check the effect of some variations of force constants that I have computed on the protein-ligand interactions. D

[gmx-users] QM/MM investigate phosphorylation/dephosphorylation in kinase

Dear all: I am preparing search reaction path in kinase by QM/MM, The kinase is a kind of autophosphorylation/autodephosphorylation enzyme , I have search many paper, but I have not find similar paper, Could somebody tell some similar paper, or give me some advice? Thank you very much!