[gmx-users] gmx-5.0 does not seem to honour plus/minus signs in topology files

Michael Brunsteiner mbx0009 at yahoo.com
Thu Jul 10 20:46:07 CEST 2014


I made myself a force field for an organic polymer using a terminology/syntax
similar to amino acids, so that i can make topoly files directly from pdb files
using pdb2gmx.
This worked nicely up to gmx-4.6.5, but when trying 5.0 pdb2gmx
complains about not finding particular atoms in a pdb file, although they are
there (only in the neighbouring residue), and then grompp gives up
because it believes to find double entries in a angle or dihedral
because the atom names in neighbouring resiues are identical.

e.g. there's an entry in the angle section of resiue 2:
"-C2 C1 C2"

the first atom is in residue 1 the second and third are in residue 2
(as indicated by the minus sign) but pdb2gmx/grompp believe that all three
names refer to atoms in residue 2 and thus grompp complanes about a duplicate
atom and givbes up ... 

Is this something that was changed in 5.0 on purpose?



Why be happy when you could be normal?

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