Re: [AMBER] constant pH simulations pemed.cuda

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Thu, 8 Mar 2018 16:19:10 +0000

Hi Jacopo,


You need to increase the limit of titrable residues in other files as well.

In particular for pmemd, you should change $AMBERHOME/src/pmemd/src/constantph.F90


You can run

grep -rnw '.' -e 'TITR_RES_C'

grep -rnw '.' -e 'MAX_TITR_RES'

in order to identify all the files that need to be changed.


In these files, you need to change:

#define MAX_TITR_RES 50

#define MAX_TITR_STATES 200

#define MAX_ATOM_CHRG 1000

or

integer, parameter :: TITR_RES_C = 50

integer, parameter :: TITR_STATES_C = 200

integer, parameter :: ATOM_CHRG_C = 1000


I recommend that you make the change in all files to avoid future problems.


HTH


Eric 


--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
________________________________
From: Jacopo Sgrignani <sgrigna.gmail.com>
Sent: 08 March 2018 15:50
To: AMBER Mailing List
Subject: Re: [AMBER] constant pH simulations pemed.cuda
Dear Vinicius
here the file.
thanks
jacopo
2018-03-08 16:48 GMT+01:00 Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>:
> Hello Jacopo,
>
>
> Could you please copy here your ph.cpin file?
>
>
> Regards,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Jacopo Sgrignani <sgrigna.gmail.com>
> Sent: Thursday, March 8, 2018 10:45:53 AM
> To: AMBER Mailing List
> Subject: [AMBER] constant pH simulations pemed.cuda
>
> Dear all
>
> I'm trying to run constant pH simulation with pmemd.cuda in Amber16 but I
> get
>
> this error:
>
> At line 164 of file constantph.F90 (unit = 23, file = 'ph.cpin')
>
> Fortran runtime error: Cannot match namelist object name 'residue:
>
>
>
> Reading other messages I understood that is due to a limit on the number of
> aminoacids that
>
> can be titrated.
>
>
> Changing the limit in the dynph.h I was able to run the calculation with
> sander but not with pmemd.cuda.
>
>
> Could you give me some advice?
>
>
> thanks
>
>
> Jacopo
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Received on Thu Mar 08 2018 - 08:30:02 PST
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