Hi Dulal,
Unlike the four GLH rotamers of glutamic acid, HIE and HID have chemically different structures. The potential energies are added up by different terms. If we run a thermodynamic integration that transfers HID to HIE, I think there will be a nonzero DELTA G between HID and HIE. Because of this, I think they might need different DELTAGREF values, even when we want their PKA to be identical.
I’m not very sure if finddgref.py can do that. I have always wanted to parameterize titratable groups with multiple protonation states and prototropic tautomer, but haven’t had a chance to try it with finddgrep.py. Maybe Dr. Cruzeiro and many other experts on this topic could help us!
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
Date: Wednesday, June 12, 2024 at 3:35 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] finddgref.py using pH-REMD
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
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<mailto: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<mailto:amber.ambermd.org>>
Date: Tuesday, June 11, 2024 at 10:31 PM
To: Carlos Simmerling <carlos.simmerling.stonybrook.edu<mailto:carlos.simmerling.stonybrook.edu>>, AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>, Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto: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<mailto:
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<mailto: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<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>).
>> The solvent pH value of replica 2 is 6.400 and was loaded from the
>> mdin file (002/002.in<https://urldefense.com/v3/__http:/002.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNIu7u6dA$>).
>> The solvent pH value of replica 3 is 6.600 and was loaded from the
>> mdin file (003/003.in<https://urldefense.com/v3/__http:/003.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNB40y_qg$>).
>> The solvent pH value of replica 4 is 6.800 and was loaded from the
>> mdin file (004/004.in<https://urldefense.com/v3/__http:/004.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNQfm3woQ$>).
>> The solvent pH value of replica 5 is 7.000 and was loaded from the
>> mdin file (005/005.in<https://urldefense.com/v3/__http:/005.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHPg89zyXA$>).
>> The solvent pH value of replica 6 is 7.200 and was loaded from the
>> mdin file (006/006.in<https://urldefense.com/v3/__http:/006.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNzmiyUDA$>).
>> The target pKa is 6.60000.
>> The temperature is 300.00 K and was loaded from the mdin file (001/
>> 001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>
>> ).
>> According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), the value of ntcnstph is 500.
>> According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), the value of nstlim is 2000.
>> According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), 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<mailto: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<mailto:babunmondal.chem.kgpian.iitkgp.ac.in>>
>> > *Sent:* Monday, June 10, 2024 10:11 PM
>> > *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>>; AMBER
>> > Mailing List <amber.ambermd.org<mailto: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<mailto: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<mailto:babunmondal.chem.kgpian.iitkgp.ac.in>>
>> > *Sent:* Monday, June 10, 2024 7:45 PM
>> > *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto: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<mailto: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<mailto:amber.ambermd.org>>
>> > *Sent:* Monday, June 10, 2024 11:24 AM
>> > *To:* AMBER Mailing List <amber.ambermd.org<mailto: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<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$> -p HIP_model.prmtop -c 001/nvtequi.ncrst -cpin
>> HIP.cpin
>> > -o
>> > 001/mdout.rep.001 -cpout 001/cpout.rep.001 -cprestrt 001/cpin.rep.001 -r
>> > 001/ncrst.rep.001 -inf 001/mdinfo.rep.001 -x 001/nc.rep.001 -rem 4
>> -remlog
>> > rem.001.log
>> >
>> > # Replica 002
>> > -O -i 002/002.in<https://urldefense.com/v3/__http:/002.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNIu7u6dA$> -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<https://urldefense.com/v3/__http:/003.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNB40y_qg$> -p HIP_model.prmtop -c 003/nvtequi.ncrst -cpin
>> HIP.cpin
>> > -o
>> > 003/mdout.rep.001 -cpout 003/cpout.rep.001 -cprestrt 003/cpin.rep.001 -r
>> > 003/ncrst.rep.001 -inf 003/mdinfo.rep.001 -x 003/nc.rep.001 -rem 4
>> -remlog
>> > rem.001.log
>> >
>> > # Replica 004
>> > -O -i 004/004.in<https://urldefense.com/v3/__http:/004.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNQfm3woQ$> -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<https://urldefense.com/v3/__http:/005.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHPg89zyXA$> -p HIP_model.prmtop -c 005/nvtequi.ncrst -cpin
>> HIP.cpin
>> > -o
>> > 005/mdout.rep.001 -cpout 005/cpout.rep.001 -cprestrt 005/cpin.rep.001 -r
>> > 005/ncrst.rep.001 -inf 005/mdinfo.rep.001 -x 005/nc.rep.001 -rem 4
>> -remlog
>> > rem.001.log
>> >
>> > # Replica 006
>> > -O -i 006/006.in<https://urldefense.com/v3/__http:/006.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNzmiyUDA$> -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<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>).
>> > The solvent pH value of replica 2 is 6.400 and was loaded from the
>> > mdin file (002/002.in<https://urldefense.com/v3/__http:/002.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNIu7u6dA$>).
>> > The solvent pH value of replica 3 is 6.600 and was loaded from the
>> > mdin file (003/003.in<https://urldefense.com/v3/__http:/003.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNB40y_qg$>).
>> > The solvent pH value of replica 4 is 6.800 and was loaded from the
>> > mdin file (004/004.in<https://urldefense.com/v3/__http:/004.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNQfm3woQ$>).
>> > The solvent pH value of replica 5 is 7.000 and was loaded from the
>> > mdin file (005/005.in<https://urldefense.com/v3/__http:/005.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHPg89zyXA$>).
>> > The solvent pH value of replica 6 is 7.200 and was loaded from the
>> > mdin file (006/006.in<https://urldefense.com/v3/__http:/006.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHNzmiyUDA$>).
>> > The target pKa is 6.60000.
>> > The temperature is 300.00 K and was loaded from the mdin file (001/
>> > 001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>
>> > ).
>> > According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), the value of ntcnstph is 500.
>> > According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), the value of nstlim is 2000.
>> > According to the mdin file (001/001.in<https://urldefense.com/v3/__http:/001.in__;!!KGKeukY!3pKlSNw2utfTq8TOTedZMZDioUpmQE4SCFn1_YDkgc86kkap7xLlnIXWwrF5IQSQGIIwIsGSL_oQK0mzW1DJsU1Mwf419GaKwGL3tDcjvHP7xrgy4g$>), 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<mailto:AMBER.ambermd.org>
>> >
>> >
>> https://urldefense.com/v3/__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__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxQzV3mdo$<https://urldefense.com/v3/__https:/nam10.safelinks.protection.outlook.com/?url=http*3A*2F*2Flists.ambermd.org*2Fmailman*2Flistinfo*2Famber&data=05*7C02*7Cvcruzeiro*40architecttherapeutics.com*7Cddb746a6a04a4fee116508dc897aa3d7*7C2443aafdae8c417b8e9f735b633fca8a*7C0*7C0*7C638536407064184189*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C&sdata=FtLDKPHN243xFY4vfpqLozSPe3gKEpgX6*2Fq*2BlL9hW90*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxQzV3mdo$>
>> > <https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$> >
>> >
>> >
>> >
>> > --
>> > *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<mailto:AMBER.ambermd.org>
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$>
>>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:AMBER.ambermd.org>
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!23w8SFca98rAp_KoEiJHyMNKTRv5AL6gWwO9Cpao15xvapbRR61bRhMh0FrwEPDs30GrEkGuYSFz1V3k4HsxJImp1T4$>
--
With regards,
Dulal Mondal,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur 721302.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 12 2024 - 11:00:02 PDT
