Hello Santo,
All seems fine in your CPIN file. I believe you are having trouble due to some limitations inside constantph.F90 that affect the maximum size of the arrays in CPIN.
Both at the top of $AMBERHOME/src/pmemd/src/constantph.F90 and of $AMBERHOME/AmberTools/src/sander/constantph.F90 you will find the following:
#define MAX_TITR_RES 50
#define MAX_TITR_STATES 200
#define MAX_ATOM_CHRG 1000
#define MAX_H_COUNT 4
MAX_ATOM_CHRG defines the limit of the charge array as 1000, and your CPIN has more charges than that (1322, to be exactly). This would explain why your CpHMD simulations work when you have less titratable residues, because the charge array is smaller, makes sense? Try to change the 4 lines above accordingly, recompile whichever MD engine you are using (sander or pmemd), and I expect your problem to be solved.
I hope this helps,
And please let me know if you need any assistance further,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Kolattukudy P. Santo <santotheophys.gmail.com>
Sent: Thursday, September 17, 2020 1:34 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] constant pH error
[External Email]
Dear Vinicius
Thanks for the reply. I attach the cpin file, which for a 20 segment chain.
Santo
On Thu, 17 Sep 2020 at 11:06, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> Hello Santo,
>
> Could you show your CPIN file that is failing?
>
> Thanks,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Sep 16, 2020, at 8:18 PM, Kolattukudy P. Santo <santotheophys.gmail.com>
> wrote:
>
> [External Email]
>
> Hello all
> I defined and parameterized some new titratable residues in
> explicit solvent for the cpHMD run. They running fine, but some combination
> of them ( into oligomers ) giving me error
> --
> At line 167 of file constantph.F90 (unit = 23, file = 'jbl2.cpin')
> Fortran runtime error: Cannot match namelist object name 0.083403
> --
> If A ,B,C are the residues, then A-B-C gives error, while A-B, B-C etc
> work fine.
> This is a strange error that I could not understand. Please advise, how to
> resolve this.
>
> Thanks a lot
> Santo
>
>
>
> --
> Best,
> KP Santo
> --------------------------------------------------------------
> Dr. Kolattukudy P. Santo
> Post doctoral Associate
> Department of Chemical and Biochemical Engineering
> Rutgers, The State University of New Jersey
> New Brunswick, New jersey
> USA
> ---------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=qSelLAEcg6JhPKHjjpZIX3TwEiyY-cg8XotdloObu_o&s=-4tcXLaIvkqnj5vRSSPcsZjqQJi_1Ymnkof9vTe1N6w&e=
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=VeHHQBR4dDXbdIaEM0vU-iuxO4-ZD_sobGeue7USK0w&s=N_-0DjFinYebMR6Sd5DZsoMmHzd-6NGM165ZcV1b4-8&e=
>
--
Best,
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2020 - 16:00:02 PDT
