[gmx-users] HETATM records of crystallized water
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 6 14:26:27 CEST 2007
> I am doing MD study on RNase A with the crystallised water included.
> The pdb file that I have contains RNase A + 188 crystallised water
> The last being the HETATM type GROMACS cannot parametrize them.
> So, it would be great if you can suggest me a way by which I can
> include these 188 crystallised water molecules and still do the MD
> study on RNase A using GROMACS 3.2.
gromacs automatically recognizes water, unless it has a very weird name.
in that case renaming it to HOH or SOL in the pdb file should do the
> On 7/6/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>> > Hi,
>> > I am working with a pdb file that has 188 crystallised molecules.
>> > How can I include these water molecules?
>> ...in what?
>> You need to describe your task with specific details before we have a
>> chance of helping you.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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