[gmx-users] fatal error, working with dimeric protein

Geraudis Mustelier gera at ict.cim.sld.cu
Wed Dec 12 00:22:27 CET 2001


I would like to apply the energy minimization to a dimeric protein molecule.
These chains (A and B), belong to the same molecule, must not be treated
independently. I would like restrain or fix all atoms except those that
belong to one residue range in the chain A.
In the pdb file generated with pdb2mgx the atoms are numbered in continuum
form, but, appear two topology files, one for each chain. These topology
files starts with number one. In contrast, make_ndx and genpr work with the
pdb file in continuum numeration, so, I obtain the following errors running

processing topology...
Fatal error: [ file "posre.itp", line 1846 ]:
Atom index (1842) in position_restraints out of bounds (1-1841)

What can I do to apply restriction to all atoms except those in particular

 MSc. Geraudis Mustelier-Portuondo

 Center of Molecular Immunology
 Calle 216 esq. A 15, Atabey, Playa
 A. Postal 16040, Havana 11600, CUBA

 email: gera at ict.cim.sld.cu

 Tel: 53-7-214335
 Fax: 53-7-335049

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