Thank you for your reply.
This is my cp_ph.in file.
On Fri, Aug 8, 2025 at 2:09 PM ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz>
wrote:
> Dear Dulal
>
> Thank you for your message.
>
> To better understand the issue and see if I can assist you with the
> calculation, could you please share your cp_ph.in input file? That would
> help me check the setup and see if any adjustments are needed.
>
> Best regards,
> Prof. Abdelatif Messaoudi
>
>
>
> Le jeu. 7 août 2025 à 08:23, Dulal Mondal via AMBER <amber.ambermd.org> a
> écrit :
>
>> 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.*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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- application/octet-stream attachment: cp_ph.in
Received on Fri Aug 08 2025 - 02:00:02 PDT
