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Bug #2477

Include statement in forcefield.itp not working

Added by Viveca Lindahl 6 months ago. Updated 6 months ago.

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

I have a top-file that includes an "external" force field called amber99sb-ildn-berger located in the working directory. The include statement is #include "amber99sb-ildn-berger.ff/forcefield.itp". gmx grompp works fine using the latest gmx 2018 (2018.2-dev-20180410-f2c9e77) but for a gmx master (2019-dev-20180410-d8f56e9) gives error

Fatal error:
Topology include file "amber99sb-ildn.ff/gbsa.itp" not found

Commenting out #include "gbsa.itp" in forcefield.itp avoids the error.

setup.tgz (1.88 MB) setup.tgz Viveca Lindahl, 04/11/2018 02:57 PM

History

#1 Updated by Viveca Lindahl 6 months ago

  • Description updated (diff)

#2 Updated by Viveca Lindahl 6 months ago

  • File deleted (setup.tgz)

#3 Updated by Viveca Lindahl 6 months ago

#4 Updated by Berk Hess 6 months ago

the gbsa files have been removed in master

#5 Updated by Viveca Lindahl 6 months ago

Berk Hess wrote:

the gbsa files have been removed in master

it wasn't obvious when quickly scanning the commit messages that something would have changed in how force fields are read. The gbsa file is in a user-provided ff directory, so how should the user change forcefield.itp?

#6 Updated by Viveca Lindahl 6 months ago

Viveca Lindahl wrote:

Berk Hess wrote:

the gbsa files have been removed in master

it wasn't obvious when quickly scanning the commit messages that something would have changed in how force fields are read. The gbsa file is in a user-provided ff directory, so how should the user change forcefield.itp?

I thought that all itps included (in forcefield.itp) would be parsed regardless of if the name (here gbsa) is recognized in some sense or not. If this is how it should be then the error message is confusing.

#7 Updated by Viveca Lindahl 6 months ago

Viveca Lindahl wrote:

Viveca Lindahl wrote:

Berk Hess wrote:

the gbsa files have been removed in master

it wasn't obvious when quickly scanning the commit messages that something would have changed in how force fields are read. The gbsa file is in a user-provided ff directory, so how should the user change forcefield.itp?

I thought that all itps included (in forcefield.itp) would be parsed regardless of if the name (here gbsa) is recognized in some sense or not. If this is how it should be then the error message is confusing.

sorry, it's me being confused. This forcefield.itp assumes the gromacs force fields have the gbsa file, I guess.

#8 Updated by Viveca Lindahl 6 months ago

  • Status changed from New to Closed

#9 Updated by Mark Abraham 6 months ago

Looks like your .top is also somehow including amber99sb-ildn.ff/gbsa.itp, which is the thing that can't work in master because that file doesn't exist in that folder. But it seems like that's not a well constructed .top. Re-open if something else comes up!

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