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

[David van der Spoel]

On 2011-04-15 11.49, Berk Hess wrote:
> 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

No.

if you do
echo 3 | pdb2gmx -f protein -ff amber99sb
it works.
This is indeed a bug in pdb2gmx.

>>>>
>>>> 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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>>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se