This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.There are two general services provided through our GLYCAM/AMBER Website. First, the Input Configurator tool provides a straight forward GUI that allows the user to generate input files for controlling MD simulations or energy minimizations of carbohydrates with AMBER 5, 7 or 8 under a variety of conditions (constant pressure, constant volume or implicit solvation). This tool greatly simplifies the tedious job of generating the cryptic input files required by the sander module. The second and more sophisticated aspect of GLYCAM/AMBER WEB is its ability to generate energy minimized 3-D structure (pdb) files for a carbohydrates, proteins or glycoproteins. Further, the necessary coordinate and topology files can be downloaded, allowing the user to perform their own MD simulations or energy minimizations using the AMBER/GLYCAM force field. This is the only online site that allows the user to upload a protein pdb file and download all of the files necessary to perform a simulation of that protein. Of particular relevance to glycobiologists is the ability to generate a pdb file for a glycoprotein structure.
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