Hello Dulal,
Did you check your prod.log file as the error message indicated? Could you please show us what it says?
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Dulal Mondal via AMBER <amber.ambermd.org>
Sent: Friday, August 8, 2025 1:55:23 AM
To: ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] findgrep.py error
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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>>
>>
>>
>>
>>
>>
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>>
>>
>>
>>
>>
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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
>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcp_ph.in%2F&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401541991657%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=tsjV%2B9LDbU8TT1c41aeYD95rjmOhb7GaPKJplQDNKM4%3D&reserved=0<http://cp_ph.in/>>). The temperature is 300.00 K and was loaded from the
>> mdin file (cp_ph.in <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcp_ph.in%2F&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401542011268%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Z1JpfVSJaqSO11VKshEqBoZjc6Tmf%2FXCa%2BA8YyOIikU%3D&reserved=0<http://cp_ph.in/>>). According to the mdin file
>> (cp_ph.in <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcp_ph.in%2F&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401542024444%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=xODLO9J8RaiWAebqpiCCmzoxVGLNkKlhx4zoM93dRzc%3D&reserved=0<http://cp_ph.in/>>), the value of ntcnstph is 500. According to
>> the mdin file (cp_ph.in <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcp_ph.in%2F&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401542043945%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=RSssIUCbTKDDGIeLm8FMmI%2Bi%2BaXugxBMO5GnZcepSpM%3D&reserved=0<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 <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fprod.nc%2F&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401542058100%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2BzINMYxlYCJQeKP9agUcVLOSurz08toG%2BIqRd4MRcjE%3D&reserved=0<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
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>>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Fri Aug 08 2025 - 19:30:03 PDT
