VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Tue Jul 24 2012 - 15:24:15 CDT

glad to help but we haven't let John Stone know if there's a bug
someplace or if this is just a labeling/usage issue w/ VMD.
IN any case -rst7 seems to do the trick.

TOm

On 07/24/2012 12:38 PM, Mahendra B Thapa wrote:
> 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>
>>
> 

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