Dear Justin,
you are definitely true. I tested with Gromacs 4.0.7 a couple of other
proteins that were correctly minimized with the same machine and the
previous version of Gromacs, and both of them stopped with the
neighborsearching error. Then, I found a way to switch to version 4.0.5 on
the sam
Dear Justin,
to add other elements to find a solution to this problem, I repeated all the
Gromacs procedure until minimization on the file PDB I used as template to
model my protein. pdb2gmx warns that 232 atoms have non-zero occupancy, it's
because there are sidechains with alternative conformatio
Anna Marabotti wrote:
Dear Justin, dear Luca,
here's the answer to your questions:
- I'm currently using the "classical" forcefield gromos96 43a1 (choice "0"
in pdb2gmx). After producing the topology, the only warning I see from
pdb2gmx is this one: WARNING: there were 0 atoms with zero occupan
Dear Justin, dear Luca,
here's the answer to your questions:
- I'm currently using the "classical" forcefield gromos96 43a1 (choice "0"
in pdb2gmx). After producing the topology, the only warning I see from
pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63
atoms with occup
4 matches
Mail list logo
