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.*
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>
>
>
> --
> *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.*
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Received on Mon Jun 10 2024 - 22:30:02 PDT
