I have found problems to run Modeller 6.2. I have a PDB file (chain A of the
PDB entry 1LDJ) that has two gaps: the first between the 56th and the 83rd
and the second between the 150th and the 156th aminoacids. I have tried to
find a command in Modeller to warn it that the PBD file has gaps, but I was
not able to do so. Even if I replace the missed aminoacids from the PDB file
in the input .ali file, the program log stills give a message error, as
follows:
"rdpir___648E> Alignment sequence not found in PDB file: 2
./cullin1.atm recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1
1"
If any of you know how to handle with this, please e-mail me.
Regards,
Fabio
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Fabio Passetti, PhD student
Instituto do Coração - HCFMUSP
Laboratório de Cardiologia e Genética Molecular
Grupo de Bioinformática
Rua Dr. Enéas de Carvalho Aguiar, 44
05403-010 São Paulo - SP - Brazil
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