[gmx-users] name of molecules at rtp archives!

[Anton Feenstra]

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

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
|(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|