There are likely formatting differences in the RST7 and CPREST files between Amber18 and Amber24. You would need to fix these in order for the restart to run smoothly. I would just restart your simulation again.
I hope this helps,
Best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
Sent: Monday, August 26, 2024 8:39 PM
To: Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18
I generate a new cpin and prmtop file using the following command.
/home/srabani/Downloads/amber24/bin/cpinutil.py -p amber18.prmtop -o amber24.cpin -resnames HIP AS4 GL4 TYR LYS -op amber24.prmtop
Now the run is running well. But It starts from 0 ns. But I already have 100 ns run. Is there any possibility to restart the run?
On Tue, Aug 27, 2024 at 8:39 AM Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in<mailto:babunmondal.chem.kgpian.iitkgp.ac.in>> wrote:
Thank you for your response. I have already completed 100 ns production run. If I use amber24 will I start from the beginning? Or is there any possible can I convert amber18 generated cpin (e.g. cpin.rep.032) to amber24 compatible cpin so that I can restart my simulation.
On Tue, Aug 27, 2024 at 5:50 AM Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>> wrote:
Hello Dulal,
Could you please try running your simulation with Amber24 and let us know if you encounter any issues? Since you’re currently using Amber18, addressing any problems might be challenging at this point since Amber18 was released several years ago. Additionally, when using Amber24, ensure you regenerate your CPIN file with cpinutils.py from Amber24.
I hope this helps!
Best regards,
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: Monday, August 26, 2024 10:16 AM
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18
Dear Experts,
I run constant pH replica exchange in amber19 using pmemd.cuda.MPI. My
titratable residue is 48 (less than 50). But I get the following error
message.
At line 167 of file constantph.F90 (unit = 23, file = '004/cpin.rep.032')
Fortran runtime error: Index 1 out of range for namelist variable stateinf
In the mdout file I see the following message.
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
|reading charge increments from file: 009/cpin.rep.032
I also upload the cpin
file.
Thanking you in advance
*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 Mon Aug 26 2024 - 23:30:01 PDT
