[gmx-users] DNA molecule builder compatible with gromacs amber ff

william Stebbeds willstebbeds at hotmail.com
Tue Apr 19 19:38:19 CEST 2011

Dear gmx-users,
this seems like a trivial problem but has driven me crazy: 
I have been trying to build a simple B-form dsDNA strand for use in MD simulations using Amber99sb. I have tried several platforms and each generates a pdb file which pdb2gmx cannot convert as it cannot understand the naming system of the other platforms.
Is there any platform that can be used to create DNA molecules with a naming system compatible with GROMACS, specifically with the Amber99sb ff?

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