Sir,
The MAPRES problem is solved , I needed to remove some atoms from the topology file to bring number less than 100 (which is hard coded value = 100). The heme molecules like heme a and heme o , contains more than 100 atomtypes (if hydrogens are included) and MAPRES limit is crossed in this case, but without Hydrogens being counted it goes pretty well.
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.
Now, I have another problem:
Running modeler gives such warnings:
-------------- iatmcls_286W> MODEL atom not classified: HEB:FE HEB iatmcls_286W> MODEL atom not classified: HEB:NA HEB
--------------
why this is so? and finally it stops due to the following error:
--------------
nselat__596E> Atom index is out of range (iatm,natm): 4338 4337 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
--------------
what can be the reason for this reason ? please provide a solution to this problem.
Thanks in advance.
sincerely,
vivek
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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