Sure, but does that match all the hydrogens that were present in the
actual charge derivation calculation? That's where the mismatch is here.
Somewhere between the charge derivation itself and the unit that is built
in leap.
All the best
Ross
On 2/12/14, 9:46 AM, "George Patargias" <gpat.bioacademy.gr> wrote:
>Hi Ross
>
>The generated AMBER prmtop and coordinates show that the structure
>has all the hydrogens.
>
>Thanks.
>George
>
>> Are you sure you haven't lost a hydrogen somewhere?
>>
>> That size looks to me of the range one might expect for a methyl
>>hydrogen
>> been lost. Especially since it is negative.
>>
>> All the best
>> Ross
>>
>>
>> On 2/12/14, 6:13 AM, "George Patargias" <gpat.bioacademy.gr> wrote:
>>
>>>Hello Jason,
>>>
>>>Thanks for these comments. You are right: my question was really about
>>> the
>>>gaff-generated charges and not about the other parameters.
>>>
>>>The ligand has 39 atoms - maybe this explains the not so small error.
>>>
>>>George
>>>
>>>
>>>> On Wed, 2014-02-12 at 12:42 +0200, George Patargias wrote:
>>>>> Hello
>>>>>
>>>>> I have created the parameters of a ligand with gaff setting the total
>>>>> charge to 0 (which is the default). When I load the generated mol2
>>>>> into
>>>>> tleap and I issue
>>>>
>>>> So `gaff' is technically everything in the force field *except*
>>>> charges.
>>>> The charge derivation is done via some other method (if you used the
>>>> default in antechamber, that would be am1-bcc). You seem to be
>>>> concerned about the charge derivation more than the force field.
>>>>
>>>>>
>>>>> charge lig
>>>>>
>>>>> I get
>>>>>
>>>>> Total unperturbed charge: -0.003001
>>>>>
>>>>> Is this a rounding issue or something?
>>>>
>>>> This is not particularly unusual in my experience (perhaps a little
>>>> bigger than I'm used to -- is your ligand large?). You can edit the
>>>> charges in the mol2 file by hand by adding 0.003001 to one of the
>>>> charges there (probably one of the 'larger' charges) to force
>>>> neutrality, or you can add 0.003001/N to each of the atoms in the
>>>> system
>>>> where N is the number of atoms in your ligand -- I don't expect either
>>>> choice to make much of a difference.
>>>>
>>>> HTH,
>>>> Jason
>>>>
>>>> --
>>>> Jason M. Swails
>>>> BioMaPS,
>>>> Rutgers University
>>>> Postdoctoral Researcher
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>Dr. George Patargias
>>>Postdoctoral Research Fellow
>>>Biomedical Research Foundation
>>>Academy of Athens
>>>4, Soranou Ephessiou
>>>115 27
>>>Athens
>>>Greece
>>>
>>>Office: +302106597568
>>>
>>>
>>>_______________________________________________
>>>AMBER mailing list
>>>AMBER.ambermd.org
>>>http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>Dr. George Patargias
>Postdoctoral Research Fellow
>Biomedical Research Foundation
>Academy of Athens
>4, Soranou Ephessiou
>115 27
>Athens
>Greece
>
>Office: +302106597568
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 12 2014 - 10:30:02 PST
