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
> >
> >
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7Cddb746a6a04a4fee116508dc897aa3d7%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638536407064184189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=FtLDKPHN243xFY4vfpqLozSPe3gKEpgX6%2Fq%2BlL9hW90%3D&reserved=0
> > <http://lists.ambermd.org/mailman/listinfo/amber>
> >
> >
> >
> > --
> > *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
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 11 2024 - 07:30:02 PDT
