On Tue, Mar 14, 2017, Maryam Hamzehee wrote:
> I am trying to do molecular dynamics simulation for my protein
> containing zinc ion. I prepared the required files using metal ion
> modelling tutorial. When I was preparing the solvated form of my protein
> after neutralizing the system I observed the following error:
> solvatebox pr TIP3PBOX 12.0 Solute vdw bounding box:
> 76.157 74.293 82.012 Total bounding box for atom centers: 100.157
> 98.293 106.012 Solvent unit box: 18.774 18.774
> 18.774 Total vdw box size: 103.148 101.645 109.547
> angstroms. Volume: 1148540.739 A^3 Mass > 527218.112 amu, Density >
> 0.762 g/cc (type - hence mass - of one or more atoms could not be
> found) Added 17722 residues.
> I can not save the *.prmtop and *.inpcrd
> file. Please kindly help me to solve this problem.
There is almost certainly some other error in the leap output, since you have
one or more atoms (perhaps Zn?) that do not have a type. I know that the leap
output is verbose, but please look through it carefully to find messages about
atom types.
If you cannot figure it out, you will need to post a small example that
illustrates the problem. (The process of trying to create a minimal example
may in fact help you localize the problem.)
....thanks...dac
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Received on Tue Mar 14 2017 - 07:30:03 PDT
