Mark Abraham wrote:
Samuel Silva Pita wrote:
Hi GMXers,
how can I find the names of the molecules that are represented at rtp
archives?
I'd tried to see at aminoacids.dat and at *bond.itp but I cannot find
the names. For example: ETH, BA, ETHH, RTOL. Which molecules are these?
Umm, residue topologies are defined in the .rtp files, and that's the
only source of information, generally. Look at the bond connectivity and
write the structure down if you can't work out what they are from the
composition. There's enough information there for a computer to describe
the topology, so there ought to be plenty for a human.
Most of the building blocks derive directly from the Gromos forcefield,
which is described in full detail in the infamous Gromos manual (4 cm /
1.5 inch worth of paper, no electronic version that I'm aware of...).
I once compiled a table describing briefly all of the building blocks in
the Gromacs forcefield, I haven't checked but it could well still be
floating online on the gromacs site...
--
Groetjes,
Anton
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
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