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?
-Justin
Thanks
Will
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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