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

[Mark Abraham]

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

>
>> -- 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
>>
>
>