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

[David van der Spoel]

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.

> -- Josh
>
> On Fri, 2011-04-15 at 12:00 +0200, gmx-developers-request at gromacs.org
> wrote:
>> Date: Fri, 15 Apr 2011 11:58:29 +0200
>> From: David van der Spoel<spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-developers] pdb2gmx, -water option, and non-standard
>>          models
>> To: Discussion list for GROMACS development
>>          <gmx-developers at gromacs.org>
>> Message-ID:<4DA816C5.7010209 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> 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
>>>>>>
>>>>>> --
>>>>>> gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>>
>>>>
>>>>
>>>
>>
>>
>> --
>> 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
>


-- 
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