[gmx-users] atom name problem between .pdb and .rtp

Paul Barrett barrett at biop.ox.ac.uk
Tue Feb 4 13:12:35 CET 2003

I am trying to model 1FIN.pdb which contains two ATP molecules. The
names of some of the the atoms in the .pdb file are different to those
in the .rtp file leading to errors, e.g. in .pdb the first ATP phospohor
atom is called "PG" and in .rtp it is called "APG".

I have edited the .pdb file to correct these differences but am left
with a problem: the longest atom names in the .rtp file are 5 characters
long, e.g.A01PG. In .pdb format atom names are up to 4 characters
(columns 13-16 according to PDB webpage). When I run gromacs it
complains that it does not recognise atom A01P. It seems to have
truncated the 5 character name I typed in to 4 characters, as it should
for .pdb format.

How can I fix this? Presumably this happens whenever anyone models ATP?

comments / hints very gratefully received

Paul Barrett

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