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
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>> >
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Received on Tue Feb 11 2020 - 08:00:02 PST
