Wrong Br and FE parameters in amber forcefields - Redmine #2711
Archive from user: Arthur Zalevsky
Br and FE are missing sigma and epsilon parameters defined in ffnonbonded.itp in amber forcefields.
Due to the formally defined parameters (bonded interactions seems valid though), systems passes grompp properly but usually explode after a short time.
amber03.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber03.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amber94.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber94.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amber96.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber96.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amber99.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber99.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amber99sb.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber99sb.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amber99sb-ildn.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amber99sb-ildn.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
amberGS.ff/ffnonbonded.itp:Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
amberGS.ff/ffnonbonded.itp:FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
(from redmine: issue id 2711, created on 2018-10-26 by gmxdefault, closed on 2018-11-01)
- Changesets:
- Revision cf9bd8e0 by Paul Bauer on 2018-11-01T07:31:43Z:
Properly define Bromine in amber forcefields
Added the proper values for Bromine to the amber forcefield definitions
in share/top/amber*/ffnonbonded.itp from the corresponding parm99.dat
file in amber itself.
Also removed the Iron parameters as they were not fully defined
and also not available in amber itself.
Fixes #2711
Change-Id: I8adb5dc1124ba39ab4a30568bd679a204dc83fc8
- Uploads:
- br_zero.log with zero epsilon and sigma
- br_zero.tpr with zero epsilon and sigma
- br_fix.tpr with fixed parameters