Dear Ross
Thanks for your quick reply. I went through the leap.log file and found
that ions08.lib was already loaded. In previous versions of Ambertools, I
never used separate definition of parameters of Na and Cl during addIons.
Then why is it so? Furthermore, I am unable to find out the solution in
manual i.e. Ambertool12, ( I went through and found nothing except addIons
and addIon2). Please, suggest me in some more details as I am unable to
find useful information regarding this error in manual and tutorial.
Regards
kshatresh
On Sun, Apr 28, 2013 at 2:33 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> On 4/27/2013 1:41 PM, Kshatresh Dutta Dubey wrote:
> > Dear Users
> >
> > I am using AmberTool 12 on centos linux. I am preparing the topology and
> > corresponding coordinate file using leap. The prmtop and crd file for
> > protein without ions is successfully saved but it is causing error when I
> > am neutralizing with Cl- ions. I am using following command and
> > corresponding error is also as-
> > *
> > *
> > *addIons kdd Cl- 0*
> > 1 Cl- ion required to neutralize.
> > Using default radius 1.50 for ion Cl-
> > Adding 1 counter ions to "kdd" using 1A grid
> > Grid extends from solute vdw + 1.50 to 7.50
> > Resolution: 1.00 Angstrom.
> > grid build: 0 sec
> > Solvent present: replacing closest with ion
> > when steric overlaps occur
> > Calculating grid charges
> > charges: 3 sec
> > (No solvent overlap)
> > Placed Cl- in kdd at (-19.18, -14.40, 6.91).
> >
> > Done adding ions.
> >> *saveamberparm kdd x.top x.crd*
> > Checking Unit.
> > WARNING: There is a bond of 7.362123 angstroms between:
> > ------- .R<ILE 11>.A<C 18> and .R<SER 12>.A<N 1>
> > WARNING: There is a bond of 3.757518 angstroms between:
> > ------- .R<ILE 11>.A<N 1> and .R<ILE 11>.A<H 2>
> > WARNING: There is a bond of 3.284000 angstroms between:
> > ------- .R<ILE 66>.A<C 18> and .R<LYS 67>.A<N 1>
> > WARNING: There is a bond of 3.147995 angstroms between:
> > ------- .R<ILE 80>.A<C 18> and .R<HIE 81>.A<N 1>
> > WARNING: There is a bond of 3.050198 angstroms between:
> > ------- .R<ILE 93>.A<C 18> and .R<VAL 94>.A<N 1>
> > WARNING: There is a bond of 3.025124 angstroms between:
> > ------- .R<ILE 157>.A<C 18> and .R<ALA 158>.A<N 1>
>
> Do you have TER cards between strands in your pdb? Long bonds can be
> accidentally drawn when strands are not separated.
>
>
> >
> > -- ignoring the warnings.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<Cl- 8929>.A<Cl- 1> Could not find type: Cl-
> > Parameter file was not saved.
>
> You need to load the ion params for the water model you are using. See
> the tutorials, the manual, or old discussions here.
>
> Bill
>
> >
> > I have used same protocol several times in previous work, but now I am
> > unable to figure out the problem. I will deeply appreciate your
> suggestion.
> >
> > Thanks in advance
> >
> > Regards
> > Kshatresh Dutta Dubey,
> > Post-doctoral Fellow, BSBE
> > IIT Kanpur
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sat Apr 27 2013 - 15:00:03 PDT
