Hello Dulal,
There is likely an issue with your input files. If you run the simulation with constant pH turned off, you should see the same error. Therefore, this does not seem to be a problem with the finddgref.py script. I recommend that you double check how you are creating the input files, visually inspect your PDB file, etc.
I hope this helps.
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
Sent: Saturday, August 9, 2025 2:25:46 AM
To: Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
Cc: AMBER Mailing List <amber.ambermd.org>; ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz>
Subject: Re: [AMBER] findgrep.py error
Thank you for responding.
For sander, the result is like below.
On Sat, Aug 9, 2025 at 1:48 PM Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>> wrote:
Hello Dulal,
Could you please share the full LOG file?
Also, what happens when you use sander? Do you see a different error?
All the 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: Saturday, August 9, 2025 1:04:22 AM
To: Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>; ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz<mailto:amessaoudi.univ-batna.dz>>
Subject: Re: [AMBER] findgrep.py error
Thank you for your response.
in pmemd, I get the following error in out file using amber24.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
On Sat, Aug 9, 2025 at 9:24 AM Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>> wrote:
Hello Dulal,
All looks good in the log file, which is weird. You should not get that error message if the Amber simulation finishes fine.
Two suggestions for you to try:
1. Use pmemd instead of pmemd.cuda to test if the error persists or any error messages appear in the output file. You may try using sander instead as well.
2. Are you using the latest Amber version?
All the 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: Friday, August 8, 2025 8:35:03 PM
To: Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>; ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz<mailto:amessaoudi.univ-batna.dz>>
Subject: Re: [AMBER] findgrep.py error
Thank you for your response. I checked the file. But I can not find the exact error. I uploaded the prod.log file.
On Sat, Aug 9, 2025 at 7:50 AM Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>> wrote:
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<mailto:amber.ambermd.org>>
Sent: Friday, August 8, 2025 1:55:23 AM
To: ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz<mailto:amessaoudi.univ-batna.dz>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] findgrep.py error
Thank you for your reply.
This is my cp_ph.in<
http://cp_ph.in/> file.
On Fri, Aug 8, 2025 at 2:09 PM ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz<mailto: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<http://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<mailto: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<http://cp_ph.in/> -o prod.log -r prod.out -p tyr.prmtop -c nvt.ncrst -r prod.ncrst
>> -x prod.nc<http://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/>
>> <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<http://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<http://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<http://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<http://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<mailto:AMBER.ambermd.org>
>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7C19c54ae7496f458f7df108ddd6595fd8%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638902401542070811%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=JGi2R9%2Br2T8JQKL52hZUMq7H9O9ugnHghq9TU45Iias%3D&reserved=0<http://lists.ambermd.org/mailman/listinfo/amber>
>>
>
--
*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.
--
With regards,
Dulal Mondal,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur 721302.
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Received on Sat Aug 09 2025 - 12:30:03 PDT
