Converting Amber pdb to GROMACS pdb to output a topology

User discussions
1

Hello,

I used GAMES and Amber to parameterize the metal ion in my enzyme. I used Acpype to convert the prmtop and inpcrd files to GROMACS gro and top files. I converted the gro file to a pdb file, and the old top file I don’t want. Now, I want to use pdb2gmx to generate a new topology file from the new pdb file, but when I run the command everything works till the code has to write out the new topology file. I get this error for Charmm forcefields:
Fatal error:
Residue ‘HIE’ not found in residue topology database
I get this error for all of the Amber forcefields:
Fatal error:
Residue ‘GU1’ not found in residue topology database
Which I know I need to convert the residue names in the new pdb file. I could do maunally, but is there a table of all of the residue conversions from AMBER (my new pdb file) to GROMACS for I can generate a new topology?

2

Amber’s HIE is CHARMM’s HSE/HISE, you can substitute the names and it should work.

GU1 doesn’t look like any standard residue though, so I wouldn’t expect it to work out of the box.