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Error : seqpos <= size()

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Error : seqpos <= size()

Dear Rossetta Users,

when I run Flexpepdock protocol, the error is : "ERROR: seqpos <= size()
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 289:.

Can someone here explain why this happenned?
I attach the input file below.

Best regards
Phan Vy

strarting.txt375.95 KB
Post Situation: 
Sun, 2014-10-05 17:20

Can you attach your command line with any flags that you used? Does the result change at all if you remove the zinc ion?

Mon, 2014-10-06 12:21

Dear everyday847,
I removed Zinc, but the error still return (same above)

This is the flag for running prepack before running Flexpepdock protocol

s starting.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database


I got starting structure from Molecular Dynamics simulation.
Thank a lot and best regard

Phan Vy

Mon, 2014-10-06 16:06

Your "occupancy" column in the PDB is zero, which means Rosetta will ignore those atoms by default. (Leading to an empty structure.)

Use the option "-ignore_zero_occupancy false" to override this behavior and use all the atom coordinates specified in the PDB.

Mon, 2014-10-06 16:46

Thank a lot for your help. It work now

Phan Vy

Mon, 2014-10-06 21:18