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Bug #410

Adaptation of amberports for gromacs 4.1 (git master) based on 4.0

Added by Alexey Shvetsov over 9 years ago. Updated over 9 years ago.

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

I made adopatation of amber ports1 for gromacs 4.1 (git master)
This adoptation based on amberports for gromacs 4.0 [2] and should be fully functional.
Patch included into this mail against git master

[1] http://ffamber.cnsm.csulb.edu/
[2] http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz

0001-Add-ffamber-ports-to-GROMACS-4.1.-http-ffamber.cnsm..patch (2.21 MB) 0001-Add-ffamber-ports-to-GROMACS-4.1.-http-ffamber.cnsm..patch amberports patch againt git master Alexey Shvetsov, 05/06/2010 03:19 PM

History

#1 Updated by Alexey Shvetsov over 9 years ago

Created an attachment (id=451)
amberports patch againt git master

#2 Updated by Erik Lindahl over 9 years ago

Hi Alexey!

Thanks for the contribution - we're about to make the Amber forcefield officially supported for Gromacs 4.5 (lots of changes so we're jumping there instead of 4.1) - there are a bit more checks to do (including against your files), but after that we'll support everything, including the new ILDN modifications from DE Shaw!

(Thus, we might not commit these files immediately, but the support will be there in 4.5)

Cheers,

Erik

#3 Updated by Alexey Shvetsov over 9 years ago

Heh. Seems initial amberff support was added to gromacs git master. But in current state it isnt included in install target. So will amber ff be released with 4.5 version?

PS I'm ready to test them on my systems =)

#4 Updated by Erik Lindahl over 9 years ago

It will be.

#5 Updated by Erik Lindahl over 9 years ago

Most of the popular Amber force fields are now present in git head, but beware that they are NOT meant for production yet - they need be tested by more people in the 4.5 beta phase first.

The new files are still based on Eric Sorin's work, but they have changed a lot to make for a cleaner implementation, and some parameters have been recalculated from Amber parmXX.dat files.

Please open a separate bugzilla if you find specific errors in those files, or if they fail validation.

#6 Updated by Alexey Shvetsov over 9 years ago

Thanks =)

I'm going to start testing them with git master codebase

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