[AMBER] problem with solvation

From: Maryam Hamzehee <maryam_h_7860.yahoo.com>
Date: Tue, 14 Mar 2017 07:21:18 +0000 (UTC)

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
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