Thank you for your reply. I run constant pH MD and constant pH REMD
simulation. In both cases I calculate the population of three protonation
states of HIS-64. The reported pKa value of His-64 is 7.1. At pH <7, HIP is
more populated and At PH >7.1 neutral (HID) form is more populated. But the
population of HIE is negligible at high pH also. I think two singly
protonation states (HID and HIE) should have the same population. Is this
correct or not?
On Wed, Jun 12, 2024 at 12:58 PM He, Amy <he.1768.buckeyemail.osu.edu>
wrote:
> Hi Dulal,
>
>
>
> I’m not very familiar with the finddgref routine. I was wondering is there
> a particular reason you wanted to equalize the two tautomeric forms of
> histidine (HID and HIE)? In the default setting, there’s a PKA difference
> of 0.6 between them and their DELTAGREF values are different, too. You can
> retrieve the information by:
>
> cpinutil.py --describe HIP
>
>
>
> Have you tried doing finddgref individually for HID and HIE? In constant
> pH MD simulations, transformation between HID and HIE is always mediated by
> HIP. So as long as the energy difference to HIP is reasonable, the
> population should be good? What do you think?
>
>
>
>
>
> *From: *Dulal Mondal via AMBER <amber.ambermd.org>
> *Date: *Tuesday, June 11, 2024 at 10:31 PM
> *To: *Carlos Simmerling <carlos.simmerling.stonybrook.edu>, AMBER Mailing
> List <amber.ambermd.org>, Vinicius Cruzeiro <
> vcruzeiro.architecttherapeutics.com>
> *Subject: *Re: [AMBER] finddgref.py using pH-REMD
>
>
>
> Thank you sir for your reply. My cpin file is like below.
> &CNSTPH
> CHRGDAT=-0.3479,0.2747,-0.1354,0.1212,-0.0414,0.081,0.081,-0.0012,-0.1513,
> 0.3866,-0.017,0.2681,-0.1718,0.3911,-0.1141,0.2317,0.7341,-0.5894,-0.3479,
> 0.2747,-0.1354,0.1212,-0.111,0.0402,0.0402,-0.0266,-0.3811,0.3649,0.2057,
>
> 0.1392,-0.5727,0.0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.2747,-0.1354,0.1212,
>
> -0.1012,0.0367,0.0367,0.1868,-0.5432,0.0,0.1635,0.1435,-0.2795,0.3339,-0.2207,
> 0.1862,0.7341,-0.5894,
> PROTCNT=2,1,1,
> RESNAME='System: Unknown','Residue: HIP 2',
> RESSTATE=0,
> STATEINF(0)%FIRST_ATOM=7, STATEINF(0)%FIRST_CHARGE=0,
> STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=18,
> STATEINF(0)%NUM_STATES=3,
> *STATENE=0.000000,DELTAGREF,DELTAGREF,*
> *PKA_CORR=6.6000,0.0000,0.0000,*
> TRESCNT=1,CPHFIRST_SOL=4, CPH_IGB=2, CPH_INTDIEL=1.0,
> /
>
> I set the STATENE Flag like this. And set pKa value 6.60,0.0,0.0.
> Is this correct?
>
> On Tue, Jun 11, 2024 at 7:54 PM Carlos Simmerling <
> carlos.simmerling.stonybrook.edu> wrote:
>
> > Vinicius can help with details, but I do suggest that you upgrade your
> > Amber version (v18 is fairly old), and make sure the Amber tests pass.
> > also keep in mind that His has 2 reference energies, not just one.
> >
> > On Tue, Jun 11, 2024 at 1:25 AM Dulal Mondal via AMBER <
> amber.ambermd.org>
> > wrote:
> >
> >> I use pmemd.MPI. I got the following error.
> >> set AMBER=/home/srabani/Downloads/amber18/bin/pmemd.MPI
> >> finddgref.py -do_parallel mpirun -np 6 -mdexec
> >> /home/srabani/Downloads/amber18/bin/pmemd.MPI -ng 6 -groupfile
> >> groupfile001
> >> -target 6.6 -bin-path /home/srabani/Downloads/amber18/bin
> >> Checking cpin file and/or cein file.
> >> We are going to find DELTAGREF for a pH titratable residue using
> Replica
> >> Exchange.
> >> The solvent pH value of replica 1 is 6.200 and was loaded from the
> >> mdin file (001/001.in).
> >> The solvent pH value of replica 2 is 6.400 and was loaded from the
> >> mdin file (002/002.in).
> >> The solvent pH value of replica 3 is 6.600 and was loaded from the
> >> mdin file (003/003.in).
> >> The solvent pH value of replica 4 is 6.800 and was loaded from the
> >> mdin file (004/004.in).
> >> The solvent pH value of replica 5 is 7.000 and was loaded from the
> >> mdin file (005/005.in).
> >> The solvent pH value of replica 6 is 7.200 and was loaded from the
> >> mdin file (006/006.in).
> >> The target pKa is 6.60000.
> >> The temperature is 300.00 K and was loaded from the mdin file (001/
> >> 001.in
> >> ).
> >> According to the mdin file (001/001.in), the value of ntcnstph is 500.
> >> According to the mdin file (001/001.in), the value of nstlim is 2000.
> >> According to the mdin file (001/001.in), the value of numexchg is
> 10000.
> >>
> >> The program will try to find a range of values for DELTAGREF
> >> automatically, as the argument -dgrefrange was not given
> >>
> >> AMBER execution #1: running 10000000 MD steps (5000 replica exchange
> >> attempts) for DELTAGREF = 0.000000 kcal/mol
> >>
> >> ERROR: The execution of AMBER using the binary
> >> /home/srabani/Downloads/amber18/bin/pmemd.MPI failed. The execution
> >> returned the following STDERR:
> >>
> >> setup_groups: MPI size is not a multiple of -ng
> >>
> >>
> >> The command executed was:
> >>
> >> mpirun -np 6 /home/srabani/Downloads/amber18/bin/pmemd.MPI -ng 6
> >> -groupfile groupfile001.temporary
> >>
> >> Check the mdout file (001/mdout.rep.001) to see what the error
> >> might
> >> be. Also check if all libraries necessary to run AMBER are properly set.
> >> The execution of finddgref.py stopped
> >> unset echo
> >>
> >> There is no generation of mdout file.
> >>
> >> On Tue, Jun 11, 2024 at 10:44 AM Vinicius Cruzeiro <
> >> vcruzeiro.architecttherapeutics.com> wrote:
> >>
> >> > Ok. I suggest you try to use pmemd.MPI instead of pmemd.cuda.MPI just
> to
> >> > see if any error messages pop up.
> >> >
> >> > Best,
> >> >
> >> > *Vinícius Wilian D. Cruzeiro, PhD*
> >> > Scientist II, Computational Chemistry
> >> > Architect Therapeutics
> >> > Twitter: @vwcruzeiro
> >> > ------------------------------
> >> > *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> >> > *Sent:* Monday, June 10, 2024 10:11 PM
> >> > *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>; AMBER
> >> > Mailing List <amber.ambermd.org>
> >> > *Subject:* Re: [AMBER] finddgref.py using pH-REMD
> >> >
> >> > Respected sir,
> >> > Thank you for your response. I check all six mdout files. All are the
> >> same.
> >> >
> >> > On Tue, Jun 11, 2024 at 10:33 AM Vinicius Cruzeiro <
> >> > vcruzeiro.architecttherapeutics.com> wrote:
> >> >
> >> > Did you check all your MDOUT files?
> >> >
> >> > *Vinícius Wilian D. Cruzeiro, PhD*
> >> > Scientist II, Computational Chemistry
> >> > Architect Therapeutics
> >> > Twitter: .vwcruzeiro
> >> > ------------------------------
> >> > *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> >> > *Sent:* Monday, June 10, 2024 7:45 PM
> >> > *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
> >> > *Subject:* Re: [AMBER] finddgref.py using pH-REMD
> >> >
> >> > No, I do not see any error messages. my out file is like below.
> >> > Ewald parameters:
> >> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> =
> >> > 1
> >> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> >> > Box X = 39.455 Box Y = 38.946 Box Z = 35.199
> >> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> >> > NFFT1 = 40 NFFT2 = 40 NFFT3 = 36
> >> > Cutoff= 10.000 Tol =0.100E-04
> >> > Ewald Coefficient = 0.27511
> >> > Interpolation order = 4
> >> >
> >> > | PMEMD ewald parallel performance parameters:
> >> > | block_fft = 0
> >> > | fft_blk_y_divisor = 2
> >> > | excl_recip = 0
> >> > | excl_master = 0
> >> > | atm_redist_freq = 320
> >> >
> >> >
> >> >
> >>
> --------------------------------------------------------------------------------
> >> > 3. ATOMIC COORDINATES AND VELOCITIES
> >> >
> >> >
> >>
> --------------------------------------------------------------------------------
> >> >
> >> > ACE
> >> > begin time read from input coords = 2300.000 ps
> >> >
> >> >
> >> > Number of triangulated 3-point waters found: 1846
> >> >
> >> > Sum of charges from parm topology file = 0.00000000
> >> > Forcing neutrality...
> >> >
> >> > On Tue, Jun 11, 2024 at 12:06 AM Vinicius Cruzeiro <
> >> > vcruzeiro.architecttherapeutics.com> wrote:
> >> >
> >> > Hello Dulal,
> >> >
> >> > Do you see any error messages at the bottom of your MDOUT files?
> >> >
> >> > Best,
> >> >
> >> > *Vinícius Wilian D. Cruzeiro, PhD*
> >> > Scientist II, Computational Chemistry
> >> > Architect Therapeutics
> >> > Twitter: .vwcruzeiro
> >> > ------------------------------
> >> > *From:* Dulal Mondal via AMBER <amber.ambermd.org>
> >> > *Sent:* Monday, June 10, 2024 11:24 AM
> >> > *To:* AMBER Mailing List <amber.ambermd.org>
> >> > *Subject:* [AMBER] finddgref.py using pH-REMD
> >> >
> >> > Dear User,
> >> >
> >> > I am trying to find the reference energy of model Histidine. My group
> >> file
> >> > is like below
> >> > # Replica 001
> >> > -O -i 001/001.in -p HIP_model.prmtop -c 001/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 001/mdout.rep.001 -cpout 001/cpout.rep.001 -cprestrt 001/cpin.rep.001
> -r
> >> > 001/ncrst.rep.001 -inf 001/mdinfo.rep.001 -x 001/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > # Replica 002
> >> > -O -i 002/002.in -p HIP_model.prmtop -c 002/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 002/mdout.rep.001 -cpout 002/cpout.rep.001 -cprestrt 002/cpin.rep.001
> -r
> >> > 002/ncrst.rep.001 -inf 002/mdinfo.rep.001 -x 002/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > # Replica 003
> >> > -O -i 003/003.in -p HIP_model.prmtop -c 003/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 003/mdout.rep.001 -cpout 003/cpout.rep.001 -cprestrt 003/cpin.rep.001
> -r
> >> > 003/ncrst.rep.001 -inf 003/mdinfo.rep.001 -x 003/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > # Replica 004
> >> > -O -i 004/004.in -p HIP_model.prmtop -c 004/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 004/mdout.rep.001 -cpout 004/cpout.rep.001 -cprestrt 004/cpin.rep.001
> -r
> >> > 004/ncrst.rep.001 -inf 004/mdinfo.rep.001 -x 004/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > # Replica 005
> >> > -O -i 005/005.in -p HIP_model.prmtop -c 005/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 005/mdout.rep.001 -cpout 005/cpout.rep.001 -cprestrt 005/cpin.rep.001
> -r
> >> > 005/ncrst.rep.001 -inf 005/mdinfo.rep.001 -x 005/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > # Replica 006
> >> > -O -i 006/006.in -p HIP_model.prmtop -c 006/nvtequi.ncrst -cpin
> >> HIP.cpin
> >> > -o
> >> > 006/mdout.rep.001 -cpout 006/cpout.rep.001 -cprestrt 006/cpin.rep.001
> -r
> >> > 006/ncrst.rep.001 -inf 006/mdinfo.rep.001 -x 006/nc.rep.001 -rem 4
> >> -remlog
> >> > rem.001.log
> >> >
> >> > I got the following error
> >> > Checking cpin file and/or cein file.
> >> > We are going to find DELTAGREF for a pH titratable residue using
> >> Replica
> >> > Exchange.
> >> > The solvent pH value of replica 1 is 6.200 and was loaded from
> the
> >> > mdin file (001/001.in).
> >> > The solvent pH value of replica 2 is 6.400 and was loaded from
> the
> >> > mdin file (002/002.in).
> >> > The solvent pH value of replica 3 is 6.600 and was loaded from
> the
> >> > mdin file (003/003.in).
> >> > The solvent pH value of replica 4 is 6.800 and was loaded from
> the
> >> > mdin file (004/004.in).
> >> > The solvent pH value of replica 5 is 7.000 and was loaded from
> the
> >> > mdin file (005/005.in).
> >> > The solvent pH value of replica 6 is 7.200 and was loaded from
> the
> >> > mdin file (006/006.in).
> >> > The target pKa is 6.60000.
> >> > The temperature is 300.00 K and was loaded from the mdin file (001/
> >> > 001.in
> >> > ).
> >> > According to the mdin file (001/001.in), the value of ntcnstph is
> 500.
> >> > According to the mdin file (001/001.in), the value of nstlim is
> 2000.
> >> > According to the mdin file (001/001.in), the value of numexchg is
> >> 10000.
> >> >
> >> > The program will try to find a range of values for DELTAGREF
> >> > automatically, as the argument -dgrefrange was not given
> >> >
> >> > AMBER execution #1: running 10000000 MD steps (5000 replica exchange
> >> > attempts) for DELTAGREF = 0.000000 kcal/mol
> >> >
> >> > ERROR: The execution of AMBER using the binary
> >> > /home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI failed. The
> execution
> >> > returned the following STDERR:
> >> >
> >> >
> >> >
> >>
> --------------------------------------------------------------------------
> >> >
> >> >
> >> > The command executed was:
> >> >
> >> > mpirun -np 6 /home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI
> >> -ng
> >> > 6 -groupfile groupfile001.temporary
> >> >
> >> > Check the mdout file (001/mdout.rep.001) to see what the error
> >> might
> >> > be. Also check if all libraries necessary to run AMBER are properly
> set.
> >> > The execution of finddgref.py stopped
> >> > --
> >> > *With regards,*
> >> > *Dulal Mondal,*
> >> > *Research Scholar,*
> >> > *Department of Chemistry,*
> >> > *IIT Kharagpur, Kharagpur 721302.*
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> >
> >> >
> >>
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> >> > <
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$
> >
> >> >
> >> >
> >> >
> >> > --
> >> > *With regards,*
> >> > *Dulal Mondal,*
> >> > *Research Scholar,*
> >> > *Department of Chemistry,*
> >> > *IIT Kharagpur, Kharagpur 721302.*
> >> >
> >> >
> >> >
> >> > --
> >> > *With regards,*
> >> > *Dulal Mondal,*
> >> > *Research Scholar,*
> >> > *Department of Chemistry,*
> >> > *IIT Kharagpur, Kharagpur 721302.*
> >> >
> >>
> >>
> >> --
> >> *With regards,*
> >> *Dulal Mondal,*
> >> *Research Scholar,*
> >> *Department of Chemistry,*
> >> *IIT Kharagpur, Kharagpur 721302.*
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$
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> >>
> >
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
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>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Jun 12 2024 - 04:00:01 PDT
