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Re: [lammps-users] Converting packmol output to lammps data file
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Re: [lammps-users] Converting packmol output to lammps data file


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 9 Oct 2017 15:54:08 -0400



On Mon, Oct 9, 2017 at 2:30 PM, renefbg <renefbg@...6901...> wrote:

Dear Andrew,

Thanks for the info. I have checked the PDB files and they are all correct. The most recent packmol version was installed to avoid the issue you mentioned.

When I open the PDB file generated by packmol in VMD, all atoms are correctly identified. When using topotools to write lammps data file (and then reading the generated file in VMD), some elements are changed (carbon becomes nitrogen, hydrogen becomes carbon etc.).

I am confused by what could be the problem, as it seems that VMD is not translating correctly the bonds lenghts. Is there any other procedure in VMD to avoid this issue?

​this seems to be a VMD/TopoTools issue and should thus be discussed on the VMD mailing list, not here.
also, without knowing the individual steps you did in detail to do the conversion and providing a suitable (small) example file, it will be difficult to provide meaningful suggestions.

axel.

 

Thanks

Rene

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.