Hello Dulal,
Do you see any error messages at the bottom of your MDOUT files?
Best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Dulal Mondal via AMBER <amber.ambermd.org>
Sent: Monday, June 10, 2024 11:24 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] finddgref.py using pH-REMD
Dear User,
I am trying to find the reference energy of model Histidine. My group file
is like below
# Replica 001
-O -i 001/001.in -p HIP_model.prmtop -c 001/nvtequi.ncrst -cpin HIP.cpin -o
001/mdout.rep.001 -cpout 001/cpout.rep.001 -cprestrt 001/cpin.rep.001 -r
001/ncrst.rep.001 -inf 001/mdinfo.rep.001 -x 001/nc.rep.001 -rem 4 -remlog
rem.001.log
# Replica 002
-O -i 002/002.in -p HIP_model.prmtop -c 002/nvtequi.ncrst -cpin HIP.cpin -o
002/mdout.rep.001 -cpout 002/cpout.rep.001 -cprestrt 002/cpin.rep.001 -r
002/ncrst.rep.001 -inf 002/mdinfo.rep.001 -x 002/nc.rep.001 -rem 4 -remlog
rem.001.log
# Replica 003
-O -i 003/003.in -p HIP_model.prmtop -c 003/nvtequi.ncrst -cpin HIP.cpin -o
003/mdout.rep.001 -cpout 003/cpout.rep.001 -cprestrt 003/cpin.rep.001 -r
003/ncrst.rep.001 -inf 003/mdinfo.rep.001 -x 003/nc.rep.001 -rem 4 -remlog
rem.001.log
# Replica 004
-O -i 004/004.in -p HIP_model.prmtop -c 004/nvtequi.ncrst -cpin HIP.cpin -o
004/mdout.rep.001 -cpout 004/cpout.rep.001 -cprestrt 004/cpin.rep.001 -r
004/ncrst.rep.001 -inf 004/mdinfo.rep.001 -x 004/nc.rep.001 -rem 4 -remlog
rem.001.log
# Replica 005
-O -i 005/005.in -p HIP_model.prmtop -c 005/nvtequi.ncrst -cpin HIP.cpin -o
005/mdout.rep.001 -cpout 005/cpout.rep.001 -cprestrt 005/cpin.rep.001 -r
005/ncrst.rep.001 -inf 005/mdinfo.rep.001 -x 005/nc.rep.001 -rem 4 -remlog
rem.001.log
# Replica 006
-O -i 006/006.in -p HIP_model.prmtop -c 006/nvtequi.ncrst -cpin HIP.cpin -o
006/mdout.rep.001 -cpout 006/cpout.rep.001 -cprestrt 006/cpin.rep.001 -r
006/ncrst.rep.001 -inf 006/mdinfo.rep.001 -x 006/nc.rep.001 -rem 4 -remlog
rem.001.log
I got the following error
Checking cpin file and/or cein file.
We are going to find DELTAGREF for a pH titratable residue using Replica
Exchange.
The solvent pH value of replica 1 is 6.200 and was loaded from the
mdin file (001/001.in).
The solvent pH value of replica 2 is 6.400 and was loaded from the
mdin file (002/002.in).
The solvent pH value of replica 3 is 6.600 and was loaded from the
mdin file (003/003.in).
The solvent pH value of replica 4 is 6.800 and was loaded from the
mdin file (004/004.in).
The solvent pH value of replica 5 is 7.000 and was loaded from the
mdin file (005/005.in).
The solvent pH value of replica 6 is 7.200 and was loaded from the
mdin file (006/006.in).
The target pKa is 6.60000.
The temperature is 300.00 K and was loaded from the mdin file (001/001.in
).
According to the mdin file (001/001.in), the value of ntcnstph is 500.
According to the mdin file (001/001.in), the value of nstlim is 2000.
According to the mdin file (001/001.in), the value of numexchg is 10000.
The program will try to find a range of values for DELTAGREF
automatically, as the argument -dgrefrange was not given
AMBER execution #1: running 10000000 MD steps (5000 replica exchange
attempts) for DELTAGREF = 0.000000 kcal/mol
ERROR: The execution of AMBER using the binary
/home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI failed. The execution
returned the following STDERR:
--------------------------------------------------------------------------
The command executed was:
mpirun -np 6 /home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI -ng
6 -groupfile groupfile001.temporary
Check the mdout file (001/mdout.rep.001) 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
--
*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%7Cddb746a6a04a4fee116508dc897aa3d7%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638536407064184189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=FtLDKPHN243xFY4vfpqLozSPe3gKEpgX6%2Fq%2BlL9hW90%3D&reserved=0<http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 10 2024 - 12:00:02 PDT
