[gmx-users] ffamber03 H0 atomtype in 4.5.1

Per Larsson per.larsson at sbc.su.se
Mon Sep 6 19:05:11 CEST 2010


This seems to be an unfortunate mistake. It should not be commented out.
Thank you for reporting this, I will fix it for the next release.


6 sep 2010 kl. 17.08 skrev William Joseph Allen:

> 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 output:
> ***
> 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,
> Joe
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