[gmx-users] name of molecules at rtp archives!
feenstra at few.vu.nl
Mon Oct 9 17:57:44 CEST 2006
Mark Abraham wrote:
> Samuel Silva Pita wrote:
>> Hi GMXers,
>> how can I find the names of the molecules that are represented at rtp
>> 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...
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