I am trying to submit a job with a specified template alignment.
The template coordinates are based off a very low resolution cryoEM map, in which we believe to have identified some domains with a known NMR structure. For the rest of the protein however, no structure is available.
Therefore, we would like to generate a model in which the location of the identified domains are specified and the rest of the model should be generated with that in mind and the PDB file has been modified accordingly and formatted according to the formatting example on the webpage.
When submitting the job, it fails with the error ‘ERROR: An error occured while reading PDB formatted threading alignment file: Residue 1 in query is M while that specified in the alignment is N.’
However, the submitted query sequence is identical to the template sequence and both start with M.
Strangely, when removing the first residue in the query (then starting with Val),the job fails with ‘ERROR: An error occured while reading PDB formatted threading alignment file: Residue 1 in query is V while that specified in the alignment is M.’
Without changing anything in the submitted PDB file, the (correct) first residue in the PDB file is identified when deleting the first residue of the query sequence?
Any ideas what could be the cause of this and how to fix it?
Cheers