[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?

[Justin A. Lemkul]

ms wrote:
> On 02/07/10 21:15, David van der Spoel wrote:
>> On 2010-07-02 22.00, Arthur Roberts wrote:
>>> Hi, all,
>>>
>>> Is there a way to protonate small molecules with gromacs without editing
>>> ffgmx2.hdb file?
>> No, but try the prodrg server.
> 
> (just to be sure) Can't one modify the .gro and .top by hand?

You can do anything you want manually, but that's a very tedious task for any 
molecule with more than a handful of atoms.

-Justin

> Massimo
> 
>>>
>>> Sincerely,
>>> Art
>>>
>>> Art Roberts
>>> 7254 Shoreline Dr. #130
>>> San Diego, CA 92122
>>> cell: 206-850-7468
>>> email: aroberts99163 at yahoo.com
>>> skype=aroberts92122
>>>
>>>
>>>
>>>
>>>
>>
>>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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