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
