[gmx-developers] Re: pdb2gmx, -water option, and non-standard models

Berk Hess hess at cbr.su.se
Mon Apr 18 09:02:44 CEST 2011

On 04/16/2011 11:26 PM, Mark Abraham wrote:
> On 16/04/2011 3:22 AM, David van der Spoel wrote:
>> On 2011-04-15 18.37, Joshua L. Phillips wrote:
>>> Thanks Daniel. I've been using the solution suggested by Berk (echo 3 |
>>> pdb2gmx ...) to do this for quite awhile, but editing the topology file
>>> using sed is probably a little safer since some forcefields have more
>>> (fewer) water models to consider than others.
>>> What I imagine being the best solution is something like:
>>> pdb2gmx -ff amber99sb -water tip4pew ...
>>> I think it is reasonable to expect that a user can edit the topology
>>> file themselves if they choose to use a water model that is not 
>>> packaged
>>> with Gromacs. However, I imagine most users would expect all water
>>> models packaged with Gromacs to be listed in the enumeration.
>>> Maybe the problem is just that tip4pew is missing from the enumeration?
>> Yes, but we don't want to enumerate hundreds of water models. 
>> Nevertheless the -water XXX should be made to work somehow.
> OK, well someone needs to do it, or file a feature request on Redmine 
> so that it doesn't get forgotten.
> Mark
I don't know if there were special reasons to use an enum for this 
instead of a string.
Changing it to a string option would resolve all issues, I think.


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