pdb2gmx
Residue 'XXX' not found
in residue topology database
This means that the force field you have
selected while running pdb2gmx does not have an entry in the residue database
for XXX. The residue database entry is necessary both for stand-alone molecules
(e.g. formaldehyde) or a peptide (standard or non-standard). This entry defines
the atom types, connectivity, bonded and non-bonded interaction types for the
residue and is necessary to use pdb2gmx to build a .top file. A residue database
entry may be missing simply because the database does not contain the residue at
all, or because the name is different.
For new users, this error appears
because they are running pdb2gmx blindly on a PDB file they have without
consideration of the contents of the file. A force field is not something that
is magical, it can only deal with molecules or residues (building blocks) that
are provided in the residue database or included otherwise.
If there is not
an entry for this residue in the database, then the options for obtaining the
force field parameters are:
see if there is a different name being used for
the residue in the residue database and rename as appropriate,
parameterize
the residue / molecule yourself,
find a topology file for the residue /
molecule and include as a .itp file,
use another force field which has
parameters available for this,
search the primary literature for
publications for parameters for the residue that are consistent with the force
field that is being used.
Long bonds and/or missing atoms
There are
probably atoms missing earlier in the .pdb file which makes pdb2gmx go crazy.
Check the screen output of pdb2gmx, as it will tell you which one is missing.
Then add the atoms in your pdb file, energy minimization will put them in the
right place, or fix the side chain with e.g. the WhatIF program.
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