Hi! 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.
Cheers /Per 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
