Thanks Jason. Your assistance has been tremendous !!!
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, April 25, 2011 2:55 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problems with constant pH calc Amber 11
The output file has the correct error message:
(NTB /= 0 && NTP /= 0) but IFBOX == 0
This combination is not supported
BOX is too small: 0.000 0.000 0.000
igb>0 is only compatible with ntb=0
*** input error(s)
Constant pH is implicit solvent *only*. Constant pressure and/or constant
volume simulations only make sense in the context of an explicit solvent
simulation (with periodic boundary conditions in AMBER). Thus, in order to
run ANY generalized Born simulation, constant pH included, you must have ntb
= 0 and ntp = 0 (in which case pres0 and taup serve no purpose).
HTH,
Jason
On Mon, Apr 25, 2011 at 11:10 AM, John Khan <johnkhan.verizon.net> wrote:
> I previously ran a heating step with the protein restrained, and it
> ran fine. When I removed the restraints and performed MD
> equilibration at constant pressure (as suggested in the tutorials), my
> code would not run (see attached *.out file; error is at the end of
> file). Can you suggest a fix ?
>
> Thank you
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Saturday, April 23, 2011 9:52 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problems with constant pH calc Amber 11
>
> On Sat, Apr 23, 2011 at 5:37 PM, John Khan <johnkhan.verizon.net> wrote:
>
> > 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
> >
>
> I would skip Step 6. The excess 0s are harmless, and cprestrt file
> formats are system-dependent (since each compiler implements fortran90
> namelists differently), and cpinutil.pl will not necessarily work for
> all cprestrt files.
>
>
> > production MD on my GPU (although not shown in my code). I hope it
> > will run !
> >
>
> Constant pH simulations are only in sander, and GPU support is only
> part of pmemd, so the constant pH part will certainly not work,
> although that functionality may be available in Amber 12.
>
> HTH,
> Jason
>
>
> > 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
> > _______________________________________________
> > 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
> _______________________________________________
> 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 Mon Apr 25 2011 - 12:30:07 PDT
