r.friedman at bioc.uzh.ch
Thu Feb 4 16:50:27 CET 2010
> fairuz zulkifli wrote:
>> Hello everybody,
>> I'm Fairuz from Malaysia.
>> I just want to ask if there is someone that have information about
>> PDB of ice and itp file of ice.
>> I only had PDB of the ice and trying to convert it into itp file
>> using GAMESS software.
> You can't. A .pdb file is a coordinate file, while an .itp is a
> parameter file (topology). The two are not interchangeable. I
> presume that you can use the parameters for water and simulate at a
> suitable temperature, though.
Not always - that depends on what you want to study.
It's very difficult to get realistic presentations of ice in MD, and the
freezing temperature of water models is usually not 273K. There are some
works on the subject, using an initial model prepared according to
geometric specifications. I remember something from Victoria Buch but
there may be newer studies around.
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