Project

General

Profile

Bug #2711

Wrong Br and FE parameters in amber forcefields

Added by Arthur Zalevsky 12 months ago. Updated 12 months ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
simple
Close

Description

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
br_zero.log (18.5 KB) br_zero.log with zero epsilon and sigma Arthur Zalevsky, 10/30/2018 09:29 AM
br_zero.tpr (428 KB) br_zero.tpr with zero epsilon and sigma Arthur Zalevsky, 10/30/2018 09:29 AM
br_fix.tpr (428 KB) br_fix.tpr with fixed parameters Arthur Zalevsky, 10/30/2018 09:30 AM

Associated revisions

Revision cf9bd8e0 (diff)
Added by Paul Bauer 12 months ago

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

History

#1 Updated by Paul Bauer 12 months ago

Hello, do you have the corresponding parameters in the native amber forcefield description?
Also, can you give a sample system tpr that triggers the unexpected behaviour, so we can tell mdrun to be able to handle this kind of error as well?
Thanks!

#2 Updated by Arthur Zalevsky 12 months ago

Here's the part from original parm99.dat

  Br          2.22    0.320              Junmei(?)

and my values for parmbsc0(chi-OL3) (which is also based on amber99sb-ildn) according to acpype conversion formulas

[ atomtypes ]
;name      at.num  mass     charge ptype  sigma      epsilon
3 Br          35      79.90    0.0000  A   3.95559e-01  1.33888e+00 ; Converted from parm99.dat

tprs are in attach (sorry for them to be quite obsolete, but they were created several years ago for this project https://www.ncbi.nlm.nih.gov/pubmed/28717247)

#3 Updated by Gerrit Code Review Bot 12 months ago

Gerrit received a related patchset '1' for Issue #2711.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~I8adb5dc1124ba39ab4a30568bd679a204dc83fc8
Gerrit URL: https://gerrit.gromacs.org/8625

#4 Updated by Paul Bauer 12 months ago

  • Status changed from New to Resolved

#5 Updated by Paul Bauer 12 months ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF