[gmx-users] This may be it, but what to do?

[Dallas B. Warren]

Marc,

> 1. Generated a  two molecule complex and saved as .pdb
> 2. Parsed the file out to retain relative coordinates
> of each molecule in separate .pdb files
> 3. Run both resulting molecules through PRODRG server
> to generate .gro files for GMX processing.

FYI, you can use the editconf script to convert a pdb file to gro.

Did you visualise the molecules at this point?

> 4. Merge molecules back together into a single complex
> .gro file (again, hoping the coordinates are
> preserved)

If you see things all messed up at this point, with them fine before
merging, then as Erik noted, you have messed up the gro file format when
merging the two molecules into one file.

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.