[gmx-users] pdb-files - atom number of individual molecules

Anton Feenstra feenstra at chem.vu.nl
Fri Jan 30 09:17:05 CET 2004

B. Nick wrote:

> Dear Gromacs-user,
> I am simulating a system of 16 chains. When I write the
> final coordinates of the system in pdb-format using

In stead of listing all your questions, I'll try to give a short summary
that may answer (some of) them.

pdb2gmx makes distinctions between Proteins, DNA, water, and all else.
For proteins and DNA, they are constructef from the topology of the building
blocks, i.e. the amino acid and nucleic acid topologies from the .rtp file.
Chains within a section of 'protein' (i.e. only amino acids), are separated
based on chain identifiers (TER fields are ignored). Other molecules, however
are assumed to consist of single 'residues', hence all consequtive sets of
atoms with the same residue name *and* number, are assumed to form one
molecule. A building block in the .rtp will be expected that must match the
residue name for this molecule in the .pdb file. This makes the '26 letter'
restriction irrelevant for non-protein molecules. Water is treated differently,
in that its topology will be included as an .itp file in the final .top file.

For a system consisting of more than 26 separate chains (like GroEL, IIRC),
I'm not sure if it is sufficient for subsequent chains to have different
identifiers, as it is for residue names & numbers. A workaround may be to
insert single water molecules in between chains (dirty, but it'll work...),
or feed the separate chains to pdb2gmx, convert the .top files to .itp
files and include them in a 'master' .top file, as pdb2gmx does automatically
for protein chains anyway.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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