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>
-- 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.
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 - 14:00:03 PDT
