[gmx-users] ffamber03 H0 atomtype in 4.5.1

William Joseph Allen wjallen at vt.edu
Mon Sep 6 17:08:20 CEST 2010

Hello Gromacs users,

I have recently set up some simulations of a peptide using the amber03 
force field in 4.5.1 and implicit solvent. When I run it through grompp, 
it gives me the following:

Program grompp-4.5.1, VERSION 4.5.1
Source code file: grompp.c, line: 870

Fatal error:
Can't do GB electrostatics; the forcefield is missing 1 values for
atomtype radii, or they might be negative
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The missing value it is referring to was also mentioned in the grompp 

GB parameter(s) missing or negative for atom type 'H0'

The 'H0' (read h-zero) atomtype only appears in glycine residues. It is 
equivalent in all ways to the 'H1' (read h-one) atomtype. But for some 
reason, in the gbsa.itp file, the 'H0' atomtype is commented out. When 
it is un-commented, grompp proceeds as normal. My question is why is 
this specific atomtype commented out in the amber03 gbsa.itp file?

Thanks in advance,


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