Helper applications
Some applications that can help you determine the geometrical properties of the system, its charge, and its density.|
Volume guesser: |
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Given the number of molecules of
each type, their molar mass and the desired density,
estimates the total volume of the system. Online.
[Click here].
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solvate.tcl: |
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With a single command solvates a protein with water and ions in
a rectangular box. Distributed alongside with the packmol
package.
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maxmin.tcl |
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Gets the maximum and minimum coordinates of the atoms
of a PDB file (or of selected atoms). TCL script.
[Click here]
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charge.tcl |
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Reads a PDB file and computes the total charge
of protein molecules in it, considering standard
protonation states. Outputs the number of charged
residues of each type and histidines.
TCL script.
[Click here]
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molarmass.tcl |
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Reads a PDB file and computes the molar mass of
some selected group of atoms.
TCL script.
[Click here]
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addter.tcl |
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Add the "TER" word between different molecules in a file
generated with multiple molecules. This is required by AMBER,
so it may be useful.
TCL script.
[Click here] This can be done automatically with packmol, by adding the "add_amber_ter" option to the input file. |