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
Received on Wed Feb 12 2014 - 10:00:03 PST
