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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Received on Sat Apr 27 2013 - 14:30:02 PDT
