Hello Christophe,
The CPIN format has changed from Amber16 to Amber18. However, you can use the flag --old-format in cpinutils.py from AmberTools18 and you will get a CPIN file compatible with Amber16.
I hope this helps,
Best,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
San Diego Supercomputer Center
Department of Chemistry and Biochemistry
University of California, San Diego
Voice: +1(858)246-5584
________________________________
From: Jardin, Christophe Dr. <Christophe.Jardin.klinikum-nuernberg.de>
Sent: Friday, July 19, 2019 4:30 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation
Dear all,
I'm trying to simulate a system wit the constant pH replica exchange method.
The system has 19 titratable residues (AS4, GL4 and HIP), for which the starting state of these residues was assigned using the '-states' flag of cpinutils.
No error was detected at this stage. The proper residues were found and the protonation states attributed as it should be.
Actually, the simulation (minimization, heating, equilibration) runs properly until the production phase starts.
But then, the following error happens:
Running multipmemd version of pmemd Amber16
Total processors = 16
Number of groups = 16
At line 164 of file constantph.F90 (unit = 23, file = './xxxx.cpin')
Fortran runtime error: Bad data for namelist object statene
=============================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 19889 RUNNING AT c103074
= EXIT CODE: 2
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=============================================
I attached the cpin file.
According to the settings, the cpin file is not modified during the minimization, heating, and equilibrations.
I already did a simulation (constant pH RE MD) for a very similar system but without assigning the starting protonation state with the '-states' flag.
In this case, the simulation ran properly.
Has anyone any suggestion what the problem can be?
Thanks a lot!
Best regards
Christophe
_
________________________________
Klinikum Nürnberg, Sitz: Nürnberg, Amtsgericht Nürnberg -Registergericht- HRA 14190, Vorstand: Prof. Dr. Achim Jockwig (Vorsitzender), Dr. Andreas Becke, Univ.-Prof. Dr. Dr. Günter Niklewski, Peter Schuh
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Received on Sat Jul 20 2019 - 11:30:03 PDT
