No worries. You are very welcome!
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
Twitter: .vwcruzeiro
On Jul 27, 2021, at 9:55 PM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
Thanks, Vinicius. I apologize for the simple and somewhat repetitive question. I thought I had increased those variables enough, but that was not the case as you pointed out.
Cphstats is working smoothly again.
Best,
Matthew
On Jul 27, 2021, at 8:43 PM, Cruzeiro, Vinicius <vcruzeiro.ucsd.edu> wrote:
*Message sent from a system outside of UConn.*
Hello Matthew,
I edited the following lines at $AMBERHOME/AmberTools/src/cphstats/constants.h :
#define TITR_RES_C 100
#define TITR_STATES_C 400
#define ATOM_CHRG_C 2000
Then I recompiled cphstats and it worked.
As I mentioned in a previous email, this kind of issue will not exist anymore after the next Amber release. You will be able to use any number of titratable residues, charges, etc, without changing the source code. There will be a new namelist, called CNSTPHE_LIMITS, in the CPIN file that is generated automatically by parmed and contains all the proper limits.
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
Twitter: .vwcruzeiro
________________________________
From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Sent: Tuesday, July 27, 2021 4:41 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Cphstats unable to read cpin
Hello Vinicius,
I just wanted to follow-up to make sure you were able to access my cpout file from the Dropbox link I provided. Please let me know if you need me to provide the file in a different way. I’ve been running the constant pH simulations in the meantime, but I’m concerned about whether the results will be useable. Again, cphstats reports "Error: Could not open or parse ../prep/prot_wic.cpin for reading!”
Best,
Matthew
On Jul 26, 2021, at 7:05 AM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
Thanks, Vinicius. Below is a link to the cpout file. It’s very large, so I’ve provided a Dropbox link instead of attaching it directly to this message.
https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fwww.dropbox.com-5Fs-5F2f7mm5wrz77u319-5Fprot-2D5Fwic.cpout-2D3Fdl-2D3D0-2526d-253DDwIGaQ-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253Dv2sP0NcXooh0AheKYAtw9Cd7J0EdSVQG4YWEXaXdqLM-2526m-253D8wpg5CzSB4aCP8qTLU1tfX2Qa7CqJnwV-5Fq3Hp-5F7vGlo-2526s-253DvKlzmEl87Khg81wWZOKK-5FPuVTpuvH2HYCm80chRjqIg-2526e-253D-26amp-3Bdata-3D04-257C01-257C-257C2e14e17ac1714c487e4908d95160c75d-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637630298366573141-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26amp-3Bsdata-3DsgQ08y8OFcYIC9YZOHyaVNqYFyRqxDYMOIDCL3nOTz8-253D-26amp-3Breserved-3D0&d=DwIGaQ&c=-35OiAkTchMrZOngvJPOeA&r=v2sP0NcXooh0AheKYAtw9Cd7J0EdSVQG4YWEXaXdqLM&m=6UhaPZ17LNtpYDb3ymllGly-vSwfmV0ZhNbRAFqGtcc&s=jPhDbkpPVPevbi71CEyZaamr9MRhfqxO2Xs1muNT3js&e=
Best,
Matthew
On Jul 26, 2021, at 2:30 AM, Cruzeiro, Vinicius <vcruzeiro.UCSD.EDU> wrote:
*Message sent from a system outside of UConn.*
CPIN seems fine. Could you please send me your CPOUT file as well so I can attempt to reproduce your issue locally?
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
Twitter: .vwcruzeiro
________________________________
From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Sent: Sunday, July 25, 2021 8:50 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Cphstats unable to read cpin
Dear Amber Community,
I’m running constant pH simulations with a large number (~100) titratable residues. Cphstats complains that the associated cpin file can’t be parsed. When I look at constants.h, I see that TITR_RES_C 200, causing me to think that the large number of residues is not the issue. I’ve attached the cpin file to this message. I’d greatly appreciate advice on how to fix this issue.
Best,
Matthew
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Received on Tue Jul 27 2021 - 20:30:02 PDT
