David,
Following up on your first point, if you do want to constrain them to
specific values in the libraries, then you could do that in the same
fashion. You can build a qin file like they do in the tutorial, or list out
the values in your resp.in file like such:
"1 -0.4157
1 7" ...
# where 1 is number of atoms, charge
# molecule 1, atom 7
Clorice
On Tue, Feb 11, 2020 at 10:34 AM Clorice Reinhardt <
clorice.reinhardt.yale.edu> wrote:
> Hi David,
> That's correct- you could either set them to the library values, or you
> can do a group constraint of those blocking groups to force them to sum to
> 0. I personally do the later option. For examples of a group restraint you
> can format it following this tutorial:
> https://ambermd.org/tutorials/advanced/tutorial1/section1.htm
>
> Hope that helps,
> Clorice
>
>
> On Tue, Feb 11, 2020 at 10:28 AM David Sáez <davidsaez.udec.cl> wrote:
>
>> Dear Clorice and Amber experts,
>>
>> It is the first time I derive charges for a central nonnatural residue.
>> According to the paper of Cieplak 1995, it must be capped with ACE and NME,
>> and those residues have predefined charges.
>>
>> Is there a way to keep the charges of ACE and NME fixed to the predefined
>> values during
>> the RESP fitting?
>>
>> To the final .lib file I should only export the data regarding the
>> central residue, not ACE and NME, right?
>>
>> Thanks!
>>
>> On Thu, Feb 6, 2020 at 8:27 PM Clorice Reinhardt <
>> clorice.reinhardt.yale.edu> wrote:
>>
>>> Hi David,
>>>
>>> I can't address the dummy atom question, but alternatively I just
>>> parameterized the tyrosine residue in the deprotonated form following the
>>> RESP procedure for the 20 canonical amino acids, created a lib file, and
>>> ran MD from the get go with that. Which circumvents any issues with QM/MM
>>> and other simulations. I'm not sure your actual end goal here, so i can't
>>> say if this is the best plan of action for you-but that's how i
>>> proceeded.
>>>
>>> Clorice Reinhardt
>>>
>>>
>>> On Thu, Feb 6, 2020 at 5:39 PM David Sáez <davidsaez.udec.cl> wrote:
>>>
>>> > Hello everyone,
>>> >
>>> > I need a deprotonated TYR in my molecular dynamics simulation. I used
>>> > parmed > changeProtState as suggested in many posts. It worked well
>>> for the
>>> > MM part, but in the QM/MM section the software still "sees" the proton
>>> of
>>> > TYR (I think it became a dummy atom during the MM simulations). Is
>>> there a
>>> > way to keep it as a dummy atom?
>>> >
>>> > Thanks
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> _______________________________________________
>>> AMBER mailing list
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>>>
>>
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Received on Tue Feb 11 2020 - 08:00:02 PST
