I am working with a protein structure I obtained from the Protein Data Bank and am trying to do MD sims with amber on Blacklight (Pittsbutgh). I am new to this system. I have been having trouble loading proteins into leap and xleap on this cluster. The FATAL ERROR warnings generated centered around atoms having no type. When I have opened xleap or tleap in the past I have never specified a force field, however- today I tried:
xleap -s -f leaprc.ff10
This time my protein loaded with very few error messages
Checking Unit.
WARNING: There is a bond of 7.264594 angstroms between:
------- .R<SER 152>.A<C 10> and .R<GLU 153>.A<N 1>
WARNING: There is a bond of 7.289787 angstroms between:
------- .R<SER 458>.A<C 10> and .R<GLU 459>.A<N 1>
-- ignoring the warnings.
However- when I went ot save the prmtop and inpcrd files, I was denied as:
Building topology.
Building atom parameters.
For atom: .R<Na+ 615>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 616>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 617>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 618>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 619>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 620>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 621>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 622>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 623>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 624>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 625>.A<Na+ 1> Could not find type: Na+
For atom: .R<Na+ 626>.A<Na+ 1> Could not find type: Na+
Parameter file was not saved.
Can someone see the problem here?
Thanks for any help
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Received on Wed Sep 05 2012 - 18:00:03 PDT
