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
Received on Wed Feb 12 2014 - 10:00:04 PST
