VMD-L Mailing List

From: Mahendra B Thapa (thapamb_at_mail.uc.edu)
Date: Tue Jul 24 2012 - 12:38:00 CDT

Dear Dr. John and Dr.Thomas

                   I am able to load my amber 12 generated mdcrd file
in VMD with " file type - AMBER7 Restart" [suggested by Dr.Thomas,
www.latech.edu/~bishop] instead of "Amber coordinates with periodic
box" .

Thank you for the help,
Mahendra Thapa

On Mon, Jul 2, 2012 at 4:22 PM, Thapa, Mahendra (thapamb)
<thapamb_at_mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: John Stone
> Sent: Monday, July 02, 2012 2:22:10 PM (UTC-06:00) Central America
> To: Thapa, Mahendra (thapamb)
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: difficulty in viewing AMBER mdcrd files
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
>