VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Sat Jul 07 2012 - 09:56:37 CDT

what you described seems like an "off by one" problem in which vmd
interpreted the bounding box information as an atom ...
or otherwise mismatched coordinate info. try loading it instead as an
"amber restart file"
This happens w/ older versions of amber too. it's just a matter of
selecting the right combo of file types to load in VMD.

TOm

On 07/02/2012 03:22 PM, John Stone wrote:
> Hi,
> Can you post a gzipped copy of your file so I can try loading it?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jul 02, 2012 at 12:56:43PM -0400, Mahendra B Thapa wrote:
>> Dear VMD users,
>>
>> I generated amber mdcrd file using amber 12
>> with the amber force field. To view the structure, I at first loaded
>> prmtop file with "file type - AMBER7 Parm" and then loaded mdcrd file with
>> " file type - Amber coordinates with periodic box". Unfortunately, VMD did
>> not produce image instead just a line like image. Interestingly when I
>> used the pdb- format , it worked fine. The question is: why VMD looks like
>> not supporting prmtop and mdcrd files.
>>
>> Thanks,
>> Mahendra Thapa
>> University of Cincinnati 

-- 
*******************************
    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823
    www.latech.edu/~bishop
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