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Task #992

Vsite parameters for DNA (AMBER)

Added by Erik Marklund almost 7 years ago. Updated over 6 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
uncategorized
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Description

There are no vsite parameters for the methyl group in thymine DNA. I have parameters for amber99sb-ildn that I could push. I have used them occasionally and successfully. In fact the only thing needed is the following constrainttype :

[ constrainttypes ]
MCH3 CM 2 0.166426

Also note that the DNA parameters are the same for several modern amber flavors.

So should I push them or is further testing required? Should I aim for 4-5-patches instead?


Related issues

Related to GROMACS - Feature #794: add .vsd virtual sites files for nucleic acidsClosed08/22/2011

History

#1 Updated by Roland Schulz almost 7 years ago

See #794 for questions.

#2 Updated by Erik Lindahl over 6 years ago

Closed, according to comments in #794.

#3 Updated by Erik Lindahl over 6 years ago

  • Status changed from New to Closed

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