Dear Jason,
Thank you for your advice.
I'll check the web thread you told.
In this case, I'd like to add ions as a
ligand
Rather than electronic neutrization.
Does addition of an ion will cause a
serious problem
Under the GB solvent?
Yours sincerely,
Kurisaki
-----Original Message-----
From: Jason Swails
[mailto:jason.swails.gmail.com]
Sent: Monday, July 09, 2012 1:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] I can prepare Na+
parameter files under LEAPRC.CONSTPH.
Ion parameters are now loaded
separately, since the "correct"
parameters depend on the water model
you're using. You will need to load the
frcmod file "frcmod.ionsjc_{water
model}" where {water model} is tip3p,
spce, or tip4pew.
However, constant pH simulations only
work currently in implicit solvent, and
ions are not used in implicit solvent
simulations. As a result, you should
not add ions to your system. Ion
effects are modelled via a Debye-Huckel
screening parameter added to the GB
model (via the saltcon input variable).
This is a helpful thread here:
http://archive.ambermd.org/201206/0313.h
tml
HTH,
Jason
On Sun, Jul 8, 2012 at 4:22 AM, kurisaki
< kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
> Dear Amber developers and users,
>
> Thank you for usual kind support.
>
> I am now trying to perform constant pH
MD.
> 'leaprc.constph' was loaded in LEaP
> and
> I just tried to save the parameter
> files.
>
> As the messages say, this leaprc file
> includes
> Several ions but the warning was
> returned.
>
> (The messages are shown below)
>
> Loading parameters:
>
/home/kurisaki/amber/amber12/dat/leap/pa
> rm/parm10.dat
> Reading title:
> PARM99 + frcmod.ff99SB +
> frcmod.parmbsc0 + OL3 for RNA
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/amino10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/aminoct10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/aminont10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/phosphoaa10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/nucleic10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/ions08.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/solvents.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/constph.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/all_prot_nucleic10.lib
> Loading library:
>
/home/kurisaki/amber/amber12/dat/leap/li
> b/cph_nucleic_caps.lib
> Loading parameters:
>
/home/kurisaki/amber/amber12/dat/leap/pa
> rm/frcmod.constph
> Reading force field modification type
> file (frcmod)
> Reading title:
> Force field modifcations for
> titrations
> Loading parameters:
>
/home/kurisaki/amber/amber12/dat/leap/pa
> rm/frcmod.protonated_nucleic
> Reading force field modification type
> file (frcmod)
> Reading title:
> Force field modifications for
> protonated nucleic acids
> Using H(N)-modified Bondi radii
>
> Loading PDB file: ./test.pdb
> total atoms in file: 4726
> Leap added 5 missing atoms according
> to residue templates:
> 5 H / lone pairs
> Checking Unit.
> WARNING: The unperturbed charge of the
> unit: 5.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> For atom: .R<Na+ 296>.A<Na+ 1> Could
> not find type: Na+
> Parameter file was not saved.
> Quit
>
> (END)
>
> This situation was not improved by
> Loading leaprc.ff99SB, additionally.
>
>
> I am most grateful if you tell me how
to
>
> Resolve this discrepancy.
>
> Yours, sincerely.
>
> Ikuo
Kurisaki
>
>
>
>
________________________________________
_______
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> AMBER.ambermd.org
>
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o/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 08 2012 - 18:30:02 PDT
