AMBER Archive (2009)

Subject: Fwd: Re: [AMBER] help with parameters for ions

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Tue Jun 02 2009 - 13:33:41 CDT

Hi again,
I have realised that Amber is not loading the new library for ions
ions08.lib, so this is the reason why the topologies are identical. I have
to do it manually and it works.
Anyway, I have now problems with the model tip4pe

I have done this:

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
loadoff ions08.lib
loadamberparams frcmod.ionsjc_tip4pew
loadamberparams frcmod.tip4pew
loadoff system.lib
addions mol Na+ 30 Cl- 30
solvatebox mol TIP4PEWBOX 8.0
saveamberparm mol solvated.top solvated.crd
quit

And I get warnings of the type;

WARNING: There is a bond of 0.149566 angstroms between:
------- .R<WAT 2606>.A<EPW 4> and .R<WAT 2606>.A<O 1>
WARNING: There is a bond of 0.150217 angstroms between:
------- .R<WAT 2607>.A<EPW 4> and .R<WAT 2607>.A<O 1>
(...)

I suppose this warnings are about the distance between the oxygen atom and
the lonely pair, are them?

I have also tried to load parm99EP.dat, but the error is similar.

Interestenly, if I look at the leap.log file, I can see some warnings:

> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: ./frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung &
Cheatham JPCB (2008)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> loadamberparams frcmod.tip4pew
Loading parameters:
/hosts/pluto/tim/SOFT/amber10/dat/leap/parm/frcmod.tip4pew
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP4P
(UNKNOWN ATOM TYPE: EP)

How could I avoid this errors?

Best wishes,

Rebeca.

-------- Original Message --------
Subject: Re: [AMBER] help with parameters for ions
Date: Tue, 02 Jun 2009 19:38:00 +0200
From: rebeca <rebeca_at_mmb.pcb.ub.es>
To: AMBER Mailing List <amber_at_ambermd.org>

Hi,thanks for the suggestion, I will change to tip4
the complete script is this one:

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
loadamberparams frcmod.ionsjc_tip3p
loadoff system.lib
addions mol Na+ 30 Cl- 30
saveamberparm mol ionized.top ionized.crd
quit

In system.lib I have a library for my system, which is a carbon nanotube
using the CA carbons included in Amber.

The topology generated ionized.top is exactly the same than that generated
with the same comands except for the loadamberparams frcmod.ionsjc_tip3p

What am I doing wrong?

Rebeca.

Hi Rebeca,

You need to show the complete script of leap. I suspect that your atom
types are different from the names in the new frcmod file.

If your concern is the crystallization of KCl, you'd better use TIP4PEW or
SPC/E water and their ions. The solubilities of TIP3P-compatible ions are
also low. We are going to publish the data soon.

On Tue, 2 Jun 2009 09:46:40 -0400, "David A. Case"
<case_at_biomaps.rutgers.edu> wrote:
> On Tue, Jun 02, 2009, rebeca wrote:
>>
>> I am doing simulations using a KCl concentration 1M and I have problems
>> of
>> crystallization of ions in the simulations. I have seen in the
literature
>> that this is normal with Amber parameters for ions.
>>
>> I have found a paper
>> "Determination of Alkali and Monovalent Ion Parameters for Use in
>> Explicitly Solvated Biomolecular Simulations"
>> S Joung, Thomas E Cheatham, J. Phys. Chem. B, Vol. 112, No. 30. (1 July
>> 2008), pp. 9020-9041.
>> http://www.citeulike.org/user/softsimu/article/3863549
>
> Frcmod files for these parameters are in the frcmod_ionsjc_* files in
> $AMBERHOME/dat/leap/parm. You can use those directly, and also see how
the
> frcmod files were created, in case you want to use your own or other
> parameters.
>
> ...hope this helps...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber 

-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona
rebeca_at_mmb.pcb.ub.es

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