Please anyone respond
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
On Thu, 7 Aug, 2025, 11:42 am Dulal Mondal, <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Dear Experts,
> I am trying to calculate the reference energy using findgrep.py.
>
> I use this command
>
>
> finddgref.py -mdexec $AMBERHOME/bin/pmemd.cuda -bin-path $AMBERHOME/bin -i
> cp_ph.in -o prod.log -r prod.out -p tyr.prmtop -c nvt.ncrst -r prod.ncrst
> -x prod.nc -cpin tyr.cpin -cpout prod.cpout -cprestrt prod.cpin
> -AllowSmallBox -dgrefrange 0.0 500.0 -log prod.dat
>
> But I get the following error.
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> * Checking cpin file and/or cein file. We are going to find DELTAGREF for
> a pH titratable residue without using Replica Exchange. The solvent pH
> value is 9.600 and was loaded from the mdin file (cp_ph.in
> <http://cp_ph.in>). The temperature is 300.00 K and was loaded from the
> mdin file (cp_ph.in <http://cp_ph.in>). According to the mdin file
> (cp_ph.in <http://cp_ph.in>), the value of ntcnstph is 500. According to
> the mdin file (cp_ph.in <http://cp_ph.in>), the value of nstlim is
> 10000000. The range of values for DELTAGREF is 0.000000 to 500.000000
> kcal/mol (given on the argument -dgrefrange) AMBER execution #1: running
> 5000 MD steps for DELTAGREF = 0.000000 kcal/molERROR: The execution of
> AMBER using the binary /home/srabani/Downloads/amber24/bin/pmemd.cuda
> failed. The execution returned the following STDERR: b'
> 0\n' The command executed was:
> /home/srabani/Downloads/amber24/bin/pmemd.cuda -AllowSmallBox -O -i
> cp_ph.in.temporary -p tyr.prmtop -c nvt.ncrst -x prod.nc <http://prod.nc>
> -inf mdinfo -o prod.log -r prod.ncrst -cpin tyr.cpin.temporary -cpout
> prod.cpout -cprestrt prod.cpin Check the mdout file (prod.log) 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*
>
> I also uploaded the cpin file.
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
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Received on Fri Aug 08 2025 - 01:30:03 PDT
