[gmx-developers] TIP4P naming

[hess at sbc.su.se]

> On 6/18/10 9:11 AM, hess at sbc.su.se wrote:
>> Yes, that would make any Gromacs or non-Gromacs tool recognize
>> MW as a hydrogen.
>>
>> It should be little effort to use proper names in the hydrogen
>> database rules for tip4p and tip5p.
>> I hoped I had finally finished fixing issues and bugs...
> The "real" solution to this problem would be to add virtual site
> database entries for tip4p and tip5p, such that pdb2gmx first adds 2 H
> according to the hdb file and then one or two vsites.

It does exactly that, except for the proper naming.
I just mailed you about this.

Berk

>>
>> Berk
>>
>>> Hi,
>>>
>>> is there any reason not to rename MW to HW3 in tip4p.gro? Renaming this
>>> would make it match to the aminoacids.rtp files. And thus pdb2gmx would
>>> accept the naming from genbox.
>>>
>>> Roland
>>>
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>>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
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