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

[Berk Hess]

On 04/15/2011 11:40 AM, David van der Spoel wrote:
> On 2011-04-15 11.37, Daniel Larsson wrote:
>> An easy solution to "choose" the water model is to just edit the 
>> output from pdb2gmx.
>>
>> sed -i 
>> 's#amber99sb-ildn.ff/tip3p.itp#/path/to/custom/topology/tip4pew.itp#' 
>> topol.top
>>
>> Daniel
>>
>>
>> On Apr 14, 2011, at 19:43 , Joshua L. Phillips wrote:
>>
>>> Hi All,
>>>
>>> pdb2gmx is a great tool and I really like the flexibility to specify
>>> different forcefields using the -ff option (great for scripting)!
>>>
>>> However, when selecting water models, I was recently disappointed that
>>> the water selection option (-water) was an enumeration because it lacks
>>> the flexibility to test novel water models. For instance, even a highly
>>> regarded model like "tip4pew" isn't specified in the enumeration.
>>>
>>> Maybe the -water option could be changed to a string (similar to 
>>> -ff) in
>>> order to allow easy selection of "non-standard" water models? I am not
>>> familiar with the technical issues that might need to be addressed, so
>>> this is just a humble suggestion.
>
> There is a file in your favorite force field directory containing the 
> water models. Just add it there.
No, this is about the pdb2gmx -ff option not supporting it.

I don't know if:
echo tip4pew | pdb2gmx
would do it.

Berk
>>>
>>> Thanks!
>>>
>>> -- 
>>> Joshua L. Phillips
>>> Ph.D. Candidate
>>> School of Engineering
>>> University of California, Merced
>>>
>>> Email: jphillips7 at ucmerced.edu
>>> Phone: (209) 723-0921
>>>
>>> -- 
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>>
>
>