Dear Amber list
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.
Thanks in advanceMaryam
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Received on Tue Mar 14 2017 - 00:30:02 PDT
