[gmx-developers] TIP4P naming

[David van der Spoel]

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.
>
> 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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>


-- 
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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se