On Wed, Aug 25, 2004 at 11:45:24AM +0300, vivek sharma wrote:
> As in your topology file you have given MASS values of some Hydrogens
> while in in RESI types you didn't mentioned Hydrogens, why this is so?
> PLease clarify.
The MASS section is the same in all of the different topology files. In
principle you could delete some of the unused atom types, but there's
little point in doing so. Hydrogens are of course defined in the
RESI sections in the all-hydrogen topology (top_allh.lib).
> Running modeler gives such warnings:
>
> --------------
> iatmcls_286W> MODEL atom not classified: HEB:FE HEB
> iatmcls_286W> MODEL atom not classified: HEB:NA HEB
This means that the FE and NA atoms in the HEB residue don't have atom
classes defined. Atom classes are defined in modlib/atmcls-melo.lib and
are used for statistical potentials
(see http://salilab.org/modeller/manual6v2/node43.html)
Since you probably don't care about loop modeling of the HEB residue,
you can ignore these warnings.
> nselat__596E> Atom index is out of range (iatm,natm): 4338 4337
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
You have defined a restraint which contains one or more atoms which
don't exist in your model. Check your restraints file.
Ben Webb, Modeller Caretaker
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