[gmx-users] Residue abbreviation list with explanations

[Dallas B. Warren]

> And what is my current issue is? What should I replace the residue
name with?

Ultimately, what ever you want to.  From the name of the file, it seems
like it is formaldehyde, which is a small molecule, and from the link I
provide you the residue name used for it is FLH.  So, convention wise,
that is probably the best name to use for it.

But, that is not going to solve your problem, since you are attempting
to use pdb2gmx to generate your topology.  And that is not going to work
because FLH will not be in the residue database, as is noted at the link
that was provided to you
(http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in
_residue_topology_database)

I would suggest you actually READ what is at URL above.  Funny enough,
on the second line it actually mentions formaldehyde, take note of what
it actually says.  Plus also take notice of the second paragraph.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.