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> 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>
> *Sent:* Friday, August 8, 2025 8:35:03 PM
> *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 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> 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>
> *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.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> * 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
> >>
> 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.*
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Received on Sat Aug 09 2025 - 01:30:02 PDT
