AMBER Archive (2006)

Subject: Re: AMBER: building a box

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Tue Nov 07 2006 - 11:49:54 CST

Please pay attention to that:

solvateoct model2 TIP3PBOX 8.0

You should mention TIP3PBOX 8.0 because that is the
water and the dimension you add it.

Best regards.

Fenghui Fan

--- kepa koldo burusco <kepaquestions_at_yahoo.es> wrote:

> [7-XI-2006]
>
> Hi amber users!!!
>
> I am trying to do something apparently "wierd" and
> amber gives me problems all the time.
>
> I have built up a molecule made of 5 units. One is
> the central unit, and the other 4 are linked to that
> one. We are trying to study the bulk behaviour of a
> liquid enterely made from molecules of the same
> type. I mean, we are trying to create a solvent box
> surrounding our molecule with lots of molecules of
> the same type. We have been doing this with xLEaP
> typing:
>
> solvatebox new_petLin new_bPl 10.0
>
> and also
>
> solvateDontClip new_petLin new_bPl 10.0
>
> (new_petLin and new_bPl are "the same molecule",
> the different unit names are to allow easier ptraj
> analysis after running Molecular Dynamics)
>
> We have tried to enlarge/reduce the box size, to
> change the molecular conformation (unfolded/folded),
> to use different versions of xLEaP (amber 7 version
> and amber 8 version)... and each time we get an
> error message similar to the one attachd to this
> mail:
>
> The "solvent" molecules directly surrounding the
> "solute" molecule appear laking some residues due to
> avoid molecular overlaping, so on new "wierd" links
> are created among distant molecules.
>
> It seems that se algorithm that solvates molecules
> expect the solvent to be a single-unit molecule...
>
> We have also tried to delete the problematic
> molecules directly from the box aided by xLEaP
> windows tools once created, but "unfortunately" the
> software complains, xLEaP exists and the shell shows
> a "segmentation fault" message...
>
> So... any idea? any help? anybody knows how I
> could build my box avoiding problems such as
> these???
>
> Thank you very much in advance for your help.
>
>
> Kepa K. Burusco
> PhD Student
> Universidad Autonoma de Barcelona
> BARCELONA (Spain)
>
>
> ---------------------------------
>
> LLama Gratis a cualquier PC del Mundo.
> Llamadas a fijos y móviles desde 1 céntimo por
> minuto.
> http://es.voice.yahoo.com>
> Welcome to LEaP!
> Sourcing leaprc: ./leaprc
> ----- Source:
> /usr/local/amber7/dat/leap/cmd/leaprc.ff99
> ----- Source of
> /usr/local/amber7/dat/leap/cmd/leaprc.ff99 done
> Log file: ./leap.log
> Loading parameters: ./parm99.dat
> Loading library:
> /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
> Loading library:
> /usr/local/amber7/dat/leap/lib/all_amino94.lib
> Loading library:
> /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /usr/local/amber7/dat/leap/lib/all_aminont94.lib
> Loading library:
> /usr/local/amber7/dat/leap/lib/ions94.lib
> Loading library:
> /usr/local/amber7/dat/leap/lib/solvents.lib
> Loading parameters: ./extraParamIQLasem.par
> Reading force field mod type file (frcmod)
> Loading library: ./kepa.lib
> Loading library: ./IQLasem_fold.lib
> Loading library: ./glum.lib
> Loading library: ./itz.lib
> > solvateDontClip new_petLin new_bPl 10.0
> Solvent has no box, so preparing by making box
> including vdw
> (Use 'setBox centers' first if box was
> pre-equilibrated)
> Solute vdw bounding box: 20.017
> 19.249 19.388
> Total bounding box for atom centers: 40.017
> 39.249 39.388
> Solvent unit box: 20.130
> 17.947 16.051
> Total vdw box size: 40.260
> 53.841 48.153 angstroms.
> Volume: 104378.304 A^3
> Total mass 20823.218 amu, Density 0.331 g/cc
> Added 83 residues.
> > saveamberparm new_petLin box_petLin.top
> box_petLin.crd
> Checking Unit.
> WARNING: There is a bond of 16.971215 angstroms
> between:
> ------- .R<li2 26>.A<C3 1> and .R<li2 28>.A<C3 1>
> WARNING: There is a bond of 23.170284 angstroms
> between:
> ------- .R<li2 67>.A<C3 1> and .R<li2 71>.A<H24 35>
> WARNING: There is a bond of 14.589751 angstroms
> between:
> ------- .R<li2 68>.A<C3 1> and .R<li2 71>.A<H13 17>
> ERROR: The unperturbed charge of the unit: 1.335000
> is not integral.
> WARNING: The unperturbed charge of the unit:
> 1.335000 is not zero.
>
> -- ignoring the error and warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Could not find angle parameter: CT - HC - CT
> Could not find angle parameter: CT - HC - CT
> Building proper torsion parameters.
> ** No torsion terms for CT-CT-HC-CT
> ** No torsion terms for HC-CT-HC-CT
> ** No torsion terms for HC-CT-HC-CT
> ** No torsion terms for CT-HC-CT-HC
> ** No torsion terms for CT-HC-CT-CT
> ** No torsion terms for CT-HC-CT-CT
> ** No torsion terms for CT-CT-HC-CT
> ** No torsion terms for HC-CT-HC-CT
> ** No torsion terms for HC-CT-HC-CT
> ** No torsion terms for CT-HC-CT-HC
> ** No torsion terms for CT-HC-CT-CM
> ** No torsion terms for CT-HC-CT-CT
> Building improper torsion parameters.
> total 352 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>

 
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