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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 19 19:53:38 CEST 2011

william Stebbeds wrote:
> 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.

It would be helpful to know what you've tried, what didn't work, etc.  Is this 
not simply a matter of find-and-replace in a text editor?

> Is there any platform that can be used to create DNA molecules with a 
> naming system compatible with GROMACS, specifically with the Amber99sb ff?

Do Amber's tools not generate compatible input, like NAB and xLeap?


> Thanks
> Will


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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