Duh... Thanks Jason!
Dean
On 10/4/11 3:43 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>--
>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 - 15:30:03 PDT
