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Solvate specifications

Information


Unique identifier OMICS_31018
Name Solvate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some pdb-files of the solute.
Output data A pdb-file of the solute plus a number of water molecules and, optionally, sodium and chloride ions placed in accordance with a Debye-Hückel-distribution.
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Helmut Grubmuller

Additional information


http://www.mpibpc.mpg.de/274655/03-How_SOLVATE_works

Solvate citations

 (4)
library_books

An electrostatic mechanism for Ca2+ mediated regulation of gap junction channels

2016
Nat Commun
PMCID: 4730032
PMID: 26753910
DOI: 10.1038/ncomms9770

[…] We used VMD 1.9.1 (ref. ) to build systems comprised of full Cx26 GJCs embedded in two POPC bilayers. We constructed each system by hydrating the protein with Solvate 1.0.1 (ref. ) and then removed the water molecules in the surrounding lipid-facing portion of the protein based on hydrophobicity and the positions of lipid-facing, aromatic amino acids. We us […]

library_books

The energy landscape of adenylate kinase during catalysis

2015
PMCID: 4318763
PMID: 25580578
DOI: 10.1038/nsmb.2941

[…] ning parameters for a fully charged ADP and for inorganic phosphate PO4H2− included in the standard force field . The system was solvated in a truncated octahedral TIP3P water box using the software Solvate (http://www.mpibpc.mpg.de/home/grubmueller/downloads/solvate/index.html) and CHARMM .Note on the choice of a classical treatment for the active site: a complete quantitative understanding of t […]

library_books

Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools

2013
Comput Struct Biotechnol J
PMCID: 3962210
PMID: 24688707
DOI: 10.5936/csbj.201302014

[…] d-specific structural information of the membrane model).The membrane is generated by combining hexagonal patches of shortly equilibrated solvated POPC or POPE bilayers. The solvation is based on the Solvate plugin from Grubmüller and Groll which generates an irregularly-shaped disordered water layer []. This resulting structure can be directly used via VMD for MD simulations.The tool, packaged wi […]

library_books

How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

2008
PLoS Comput Biol
PMCID: 2242828
PMID: 18282082
DOI: 10.1371/journal.pcbi.0040024

[…] All the simulations were carried out in explicit water. The periodical TIP3 water box was created using the program VMD plugin solvate [] The system was neutralized by adding Na+- or Cl−-ions to the system using VMD autoionize-plugin. The systems used in the simulations are summarized in .Since efficient arrangement of water […]

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