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.
* 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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- application/octet-stream attachment: prod.dat
- application/octet-stream attachment: tyr.cpin
Received on Wed Aug 06 2025 - 23:30:02 PDT
