Use the restart7 format. Coordinates with box is for a trajectory.
HTH,
Jason
On Tue, Oct 4, 2011 at 4:35 PM, Dean Cuebas <deancuebas.missouristate.edu>wrote:
> Dear amberers,
>
> I have successfully created a solvent box containing many solvent
> molecules using packmol.
>
> In xleap I used:
>
> setbox benbox vdw 2
>
> To generate the periodic box, and it looks fine using:
>
> Edit benbox
>
> But upon loading the prmtop (Amber7 format) and the crd file (Amber
> coordinates with periodic box) into VMD
> the connections are all messed up. (See attached file)
>
> Any hints?
>
> The last few lines of the periodic .crd file are:
>
> 41.2660000 29.6810000 44.4370000 41.2710000 28.8110000 45.5290000
> 42.1650000 29.0160000 46.5820000 43.0540000 30.0920000 46.5430000
> 43.7420000 31.8010000 45.4190000 42.1510000 31.4350000 43.5470000
> 40.5690000 29.5210000 43.6170000 40.5780000 27.9730000 45.5600000
> 42.1680000 28.3380000 47.4330000 43.7500000 30.2520000 47.3620000
> 103.8160000 103.5940000 103.8160000 90.0000000 90.0000000 90.0000000
>
> Thanks in advance!!
>
> DeanDr. Dean Cuebas, Associate Professor of Chemistry
> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
>
>
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 14:00:05 PDT
