Jason:
Thanks for the explanation !! I will try to reduce the number of titratable
residues to <= 50, and set ntcnstph=1. I will assume that my steps
(outlined in the first e-mail) are OK. Additionally, I would like to run my
production MD on my GPU (although not shown in my code). I hope it will run
!
Thanks,
John
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Saturday, April 23, 2011 8:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problems with constant pH calc Amber 11
You are titrating 318 residues, which is an insanely large number. There is
a limit of 50 titratable residues hard-coded in sander (see
$AMBERHOME/src/sander/dynph.h, the preprocessor define TITR_RES_C). Thus,
once it hits the 50th residue, it interprets the *next* value as another
namelist variable (Residue...), hence your error.
Note that by default, cpinutil will label *every* AS4, GL4, LYS, TYR, and
HIP for titration (and your system has 318 of these!). Use the
-resnum/-resname flags to tag which residues you want to titrate
specifically.
If you want to titrate all of them, though, note that you will have to
choose a very small ntcnstph (since it only attempts to change ONE residue
each time!) so that each residue is sampled often enough. Even ntcnstph=1
will choose each residue less frequently than the original paper (2004
Mongan, et. al.) suggested.
Also, each step that you need to evaluate a protonation state change
requires that you perform *two* electrostatic calculations (one for each
state), which will take nearly twice as long (since the non-bonded
calculations are the most expensive part.
HTH,
Jason
On Sat, Apr 23, 2011 at 4:55 PM, John Khan <johnkhan.verizon.net> wrote:
> Jason:
>
> Sorry, I forgot to attached cpin file (see attached). Also, I am
> using AmberTools 1.4 (did not want to upgrade to 1.5 yet, but I will
> if there is an immediate benefit for this work).
>
> Thanks,
> John
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Saturday, April 23, 2011 7:12 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problems with constant pH calc Amber 11
>
> On Sat, Apr 23, 2011 at 3:22 PM, John Khan <johnkhan.verizon.net> wrote:
>
> > I have been unsuccessful at setting up constant pH calculations with my
> > protein. I am using Amber 11. I would greatly appreciate assistance
> with
> > the following:
> >
> > 1) Review the steps below and let me know if my setup is OK (not
> sure
> > whether all steps are necessary),
> >
> > 2) I am currently encountering the following error when attempting
> to
> > perform STEP 5:
> >
> > At line 1359 of file _mdread.f (unit = 18, file =
> > 'cpin_1')
> >
> > Fortran runtime error: Cannot match namelist object name 'residue:
> >
>
> This looks like a problem with your cpin file.
>
>
> >
> >
> >
> > The cpin_1 file is attached. I am hoping to resolve these issues so
> > that I can live to see another sunrise.
> >
>
> I think you forgot to attach it.
>
> Also, are you using AmberTools 1.5 or AmberTools1.4? AmberTools 1.5
> uses cpinutil.py instead of cpinutil.pl...
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 23 2011 - 18:00:03 PDT
