[gmx-users] Can NAMD simulation solve the problem of coordinate clash in a structural model?

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 13 13:26:17 CEST 2015

Hi Yeping Sun,

If the coordinates are garbled (what are serious coordinate clashes?),
you'll have a hard time with either NAMD or Gromacs.



On Mon, Apr 13, 2015 at 6:05 AM, sunyeping <sunyeping at aliyun.com> wrote:

> Dear all,
> I modelled a structural model of a complex containing two large proteins.
> There are serious coordinate clashes between these two proteins in the
> model. Can I expect to do Gromacs simulation to solve the problem of
> cooridnate clash and obtain a more rational model?
> Best regards,
> Yeping Sun
> Institute of Microbiology, Chinese Academy of Sciences
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Tsjerk A. Wassenaar, Ph.D.

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