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I am calculating the ASA of some virus structures downloaded from VIPERdb.
I get the following error when processing some of the 'full capsid'
structures (after tweaking MAXNET as appropriate)...
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1ej6_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 34487
*** warning: unknown form factor encountered
*** position unavailable, serial number 34487
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1ej6_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 34487
*** warning: unknown form factor encountered
*** position unavailable, serial number 34487
... (and many many more).
I tried Googling, but I couldn't find the cause of this error. Following
the errors (many thousands), the ASA appears to be calculated correctly
(for at least some of the files that I have). Actually the above
structure in particular is problematic in other ways...
ERROR: Dimension of parameter MAXNET is too small
Currently it is : 200000000
Needs to be at least: 1368998631
Which I think is impossibly large - Not sure though.
My question is, what is this warning? Is it safe to ignore? Is it
related to issues with Areaimol or rather the structure from VIPERdb?
I had thought this warning was related to 'ALT LOC' codes in the files,
for example,
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 668
*** warning: unknown form factor encountered
*** position unavailable, serial number 668
atom type found and not recognised =
THR A 13
$TEXT:Warning: $$ comment $$
WARNING: Unknown atom type: adding to list with default radius 1.8 A
$$
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 669
*** warning: unknown form factor encountered
*** position unavailable, serial number 669
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 670
*** warning: unknown form factor encountered
*** position unavailable, serial number 670
....
The above warnings appear to be co-localized with 'alternate location
codes' in the PDB. How does Areaimol handle AltLocs (and Icodes)?
Cheers,
Dan.
