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Bug #1395

rtp errors gromos and opls

Added by David van der Spoel almost 4 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Category:
-
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

As reported by

for the COOH terminal group one of the angles (the one including two carbons and the oxygen which carries the hydrogen) does not get overwritten by aminoacids.c.tdb.

Ok, somewhat slower:
Used ASPH as a test molecule and chose a -COOH capping group.

From aminoacids.rtp:

[ ASPH ]
[ atoms ]
...
C C 0.450 3
O O -0.450 3
...
[ angles ]
; ai aj ak gromos type
...
CA C O ga_30
...

From aminoacids.c.tdb:

[ COOH ]
[ replace ]
C C C 12.011 0.33
O O OA 15.9994 -0.288
OXT OT O 15.9994 -0.45
...
[ angles ]
O C OT ga_33
C O HO ga_12
CA C O ga_19
CA C OT ga_30

This mean that from [ASPH] the atom named O with the type O should exchange by an atom named O with the typ OA.
Additionally the angle for CA-C-O should change form ga_30 to ga_19

Result from pdb2gmx:

; It was generated using program:
; pdb2gmx - VERSION 4.6.5
;
; Command line was:
; pdb2gmx -f asp.pdb -o asp.gro -p asp.top -asp -ter
...
; Include forcefield parameters
#include "gromos53a5.ff/forcefield.itp"
...
[ atoms ]
...
10 C 1 ASPH C 4 0.658 12.011 ;
11 O 1 ASPH OT 4 -0.45 15.9994 ;
12 OA 1 ASPH O 4 -0.611 15.9994 ;
...
[ angles ]
...
4 10 11 2 ga_30
4 10 12 2 ga_30
...

First line from the posted [angle] is the right angle with the atom named OT.
In the second line we have still the angle from [ASPH] which doesn't get replaced by the angle from [COOH].

I tested this with GMX 4.6.5 and GMX 4.0.7 -> Think every version from GMX 4.X.Y series is affected.
Also tested it with the gromos53a5, gromos53a6, gromos43a1 force fields -> Think every gromos force field might be affected.

for GMX 4.0.7 and GMX 4.6.5 is a typo in the aminoacids.rtp file (but i would assume that it affects the whole 4.X.Y series).

[ ASPH ]
[ atoms ]
...
OD1 opls_269 -0.530 3
OD2 opls_268 -0.440 4
HD2 opls_270 0.450 4
...

The charges of OD1 and OD2 should be exchanged (from ffnonbonded.itp):

opls_268   OH   8  15.99940    -0.530   ...
opls_269 O_3 8 15.99940 -0.440 ...

For GLUH and the COOH terminal group everything is fine.

Associated revisions

Revision 592f8422 (diff)
Added by Rossen Apostolov over 3 years ago

Fixed typo in oplsaa ASPH charges.

Part of #1395.

Change-Id: I03c88c8377affadc629c7b9a04d5e8ddd1cb946a

Revision 8ebd438f (diff)
Added by Erik Lindahl over 3 years ago

Make sure duplicates bondeds are set from hackblocks

Previously the rtp file could end up containing two
entries when the N/C termini databases added interactions.
These were then quicksorted, which could make the
assignment random. We now check for duplicates and
discard the rtp entry in favor of the hackblock.

Fixes #1395.

Change-Id: I505cfbb7e6c8e8050e6e2935cc417e49a515d8d8

History

#1 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1395.
Uploader: Rossen Apostolov ()
Change-Id: I03c88c8377affadc629c7b9a04d5e8ddd1cb946a
Gerrit URL: https://gerrit.gromacs.org/3630

#2 Updated by Rossen Apostolov over 3 years ago

The patch above fixes only the opls typo. I don't know what's cause of the first part of the report.

#3 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1395.
Uploader: Erik Lindahl ()
Change-Id: I505cfbb7e6c8e8050e6e2935cc417e49a515d8d8
Gerrit URL: https://gerrit.gromacs.org/3656

#4 Updated by Erik Lindahl over 3 years ago

  • Status changed from New to Fix uploaded

#5 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1395.
Uploader: Rossen Apostolov ()
Change-Id: I8045d4ae8cde68160fd3590476a7b21cec2f0810
Gerrit URL: https://gerrit.gromacs.org/3679

#6 Updated by Erik Lindahl over 3 years ago

  • Status changed from Fix uploaded to Resolved

#7 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

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