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Bug #1755

gromacs topology file generated with amber99sb-ildn force field

Added by Tairan Yuwen almost 2 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
High
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
the same issue is also observed on 5.0.2
Affected version:
Difficulty:
uncategorized
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Description

The amber99sb-ildn force field applies several special 'define' commands to include the ILDN dihedral angle corrections over original amber99sb force field. For each residue among Ile/Leu/Asp/Asn there are several additional dihedral angle correction terms, but the topology file generated with gromacs 5.0.5 only includes the first term. This bug is also observed on gromacs 5.0.2, but not in old version of gromacs (4.5.5). The topology files generated based on 1UBQ using old and newer versions of gromacs are attached.

topol.top.5.0.5 - topology file generated with gromacs 5.0.5 (350 KB) Tairan Yuwen, 06/24/2015 07:09 AM

topol.top.4.5.5 - topology file generated with gromacs 4.5.5 (358 KB) Tairan Yuwen, 06/24/2015 07:09 AM

hackblock.patch View - Patch to fix the issue (1.86 KB) Shun Sakuraba, 06/25/2015 11:15 AM


Related issues

Duplicates GROMACS - Bug #1704: Multiple dihedrals v5.0.2 Closed
Duplicated by GROMACS - Bug #1778: gromacs 5 pdb2gmx doesn't pick up multiple torsions additive torsions in AMBER99sb-ILDN Closed 07/14/2015

Associated revisions

Revision 910e8ed9 (diff)
Added by Erik Lindahl almost 2 years ago

Fix bug removing multiple dihedrals in main rtp entries

The Gromacs-5.0 series has had a serious bug where pdb2gmx
would only consider the first entry when several explicit
bonds were listed for the same atoms in an RTP entry. Older
topologies have worked fine.

Fixes #1704, #1755.

Change-Id: I0b34aeb905dab8ea66196cabc0745583ef6d7209

History

#1 Updated by Shun Sakuraba almost 2 years ago

The problem seems to exist in constructing hackblock, where the entries with the identical atom names are merged (i.e. erased).
Attached patch seems to fix the problem but I don't know whether this is a correct solution.

#2 Updated by Tairan Yuwen almost 2 years ago

Shun Sakuraba wrote:

The problem seems to exist in constructing hackblock, where the entries with the identical atom names are merged (i.e. erased).
Attached patch seems to fix the problem but I don't know whether this is a correct solution.

Thanks a lot. I tested that patch and now it could produce correct topology file with amber99sb-ildn force field.

#3 Updated by Erik Lindahl almost 2 years ago

  • Status changed from New to Fix uploaded

I believe this has already been fixed by https://gerrit.gromacs.org/#/c/4772/1 .

#4 Updated by Erik Lindahl almost 2 years ago

  • Duplicates Bug #1704: Multiple dihedrals v5.0.2 added

#5 Updated by Erik Lindahl almost 2 years ago

Confirmed - the above change fixes it. Apologies that this affects Amber99sb-ildn too.

#6 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #1755.
Uploader: Erik Lindahl ()
Change-Id: I0c34aeb905dab8ea66196cabc0745583ef6d7210
Gerrit URL: https://gerrit.gromacs.org/4797

#7 Updated by Erik Lindahl almost 2 years ago

The link in comment 6 had an incorrect change-id. Here's the correct one: https://gerrit.gromacs.org/#/c/4772/

#8 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Fix uploaded to Resolved

#9 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

This one was important, so we'll make a special announcement of it with a new 5.0.x version.

#10 Updated by Teemu Murtola almost 2 years ago

  • Duplicated by Bug #1778: gromacs 5 pdb2gmx doesn't pick up multiple torsions additive torsions in AMBER99sb-ILDN added

#11 Updated by Berk Hess almost 2 years ago

I did some analysis to estimate what the effect is of the pdb2gmx bug on simulations with amber99sb-ildn.
With amber99sb-ildn the dihedrals that are modified with respect to amber99sb are added as a series expansion. This effect of this bug is that only the first, more important, term in the expansion is included. The result is that these modified dihedral potentials are in between amber99sb and amber99sb-ildn, most roughly half-way in between, in particular in terms of trans-gauche energy differences. Only the torsion_ASP_N_CA_CB_CG shows a lower gauche energy than both amber99sb and amber99sb-ildn. So I ran a simulation of Ala-Asp-Ala with all three force-fields to check sidechain conformations. The ensemble of amber99sb-ildn with bug ends up in between amber99sb and amber99sb-ildn. So in conclusion, this bugs caused amber99sb-ildn to generate ensembles that are (probably half-way) in between amber99sb and amber99sn-ildn. I have not seen evidence for new states that are not present in either amber99sb or amber99sb-ildn.

A fix has been submitted, but in the meantime pdb2gmx of 4.6 can be used to generate topologies for use with grompp and mdrun of 5.0.

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