Hello Divya,
When you say CPIN file for a particular frame, I suspect you refer to having the protonation states of that particular frame as initial condition in your CPIN file, is that right? If so, this is precisely what the CPRESTRT file does for you.
Keep in mind that you can know all protonation states at any frame of your trajectory from the data in the CPOUT file. There is even a script that allows you to visualize your protonation states on VMD (see VMD_pH.py in
https://ambermd.org/tutorials/advanced/tutorial18/section4.htm ).
I hope this helps,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
________________________________
From: Divya Rai via AMBER <amber.ambermd.org>
Sent: Monday, November 21, 2022 6:44 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Generation of CPIN in CpHMD simulations
Hello everyone,
I wanted to know while doing Constant pH MD simulation in explicit solvent
whether there is anyway one can generate cpin files for a particular frame?
Any lead would be appreciated.
Regards,
Divya Rai
Research scholar
IIT Kharagpur
--
*Regards,*
*Divya Rai*
*Research Scholar*
*Department of Chemistry*
*IIT Kharagpur*
[Linkedin <https://www.linkedin.com/in/divyaarai/>]
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Received on Mon Nov 21 2022 - 08:00:02 PST
