Hello Ada,
What you want to do is possible. Once you have the prmtop file with CHARMM parameters set, the only issue I foresee is that you would need to recompute the reference energies to be used in the constant pH input file (CPIN) and you would possibly need to rewrite the charges of each protonation state in this same file in order to match with CHARMM charges. AmberTools18 has a new tool called finddgref.py that can help you with the reference energy calculations (see page 489 of the Amber18 manual). I suggest you to also take a look at section 22.5 of the Amber18 manual because it has information that can potentially help you when preparing your new CPIN file.
Please let me know if you have any questions further,
All the best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Chen Yifan <ychen257.outlook.com>
Sent: Friday, April 5, 2019 2:51 PM
To: amber.ambermd.org
Subject: [AMBER] Can Amber constant pH run with CHARMM force field?
Hello Amber people,
I’m running some simulation with the Amber constant pH method in explicit solvent (which is actually hybrid). But since my system behaved weird in Amber force field ff14SB, I am thinking of using the CHARMM force field for the explicit part of the Amber constant pH method. Does anyone have experience with this? Is it possible? What should I do?
Any advice is appreciated! Thank you in advance!
Regards,
Ada
----------------------------------------------------
Ada Yifan Chen
Graduate student
Bloomberg 315
Department of Physics and Astronomy
Johns Hopkins University
3701 San Martin Drive
Baltimore MD 21218
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=9lG24IdZw9_TH8qMcC0Us-xdIoA8I7SPEjwYE8WW1Fo&s=xgsk-2ZxTDP6G1sz1k88DX30x3rdOsmUdipTFzYRnr4&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 05 2019 - 16:30:03 PDT
