Thank you Vinicius. Now I am getting back to this again. I am trying to
find the DELTAGREF for this system with :
PROTCNT=0,1,1,2,
RESNAME='System: Unknown','Residue: UPP 2',
RESSTATE=0,
STATEINF(0)%FIRST_ATOM=5, STATEINF(0)%FIRST_CHARGE=0,
STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=111,
STATEINF(0)%NUM_STATES=4,
STATENE=0.000000,DELTAGREF,DELTAGREF,DELTAGREF,
PKA_CORR=0.0000,2.4500,3.9600,3.9600,
Now the finddgref.py gives the following error
ERROR: The positions that have DELTAGREF on the STATENE flag must have the
same value on the corresponding positions at the PROTCNT or ELECCNT flag on
your cpin or cein file. Please fix that and run the program again.
The execution of finddgref.py stopped
So how can i find all energies corresponding to each protonation states ?
Thank you
Santo
On Wed, 2 Sep 2020 at 23:31, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> This is possible. Take a look at what is done for the residue HIP.
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Sep 2, 2020, at 7:36 PM, Kolattukudy P. Santo <santotheophys.gmail.com>
> wrote:
>
> [External Email]
>
> Hello all
>
> I want to define/parameterize a non standard residue with two
> carboxylic groups, having different pkas for each group's protonation.
> Is it possible to define in AMBER, a titratable residue with multiple
> protonation sites having different pkas, such as pka1, pka2 ?
> I can see that there are residues with multiple protonation states (like
> PRN) defined, but all states have the same pka.
>
> Thank you
>
> --
> Best,
> KP Santo
> --------------------------------------------------------------
> Dr. Kolattukudy P. Santo
> Post doctoral Associate
> Department of Chemical and Biochemical Engineering
> Rutgers, The State University of New Jersey
> New Brunswick, New jersey
> USA
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--
Best,
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
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Received on Mon Sep 07 2020 - 09:00:03 PDT
