VMD-L Mailing List

From: Puspita Halder (puspitah_at_gmail.com)
Date: Thu Jun 26 2014 - 09:15:40 CDT

Hi,

Thanks for your comments. I did not strip out the water molecules of
my dcd file. Do u think that would help analyzing the secondary
structure of the big dcd file using sscache? I am carrying out other
analyses (e.g., rmsd, radius of gyration, sasa etc.) of my large dcd
file using bigdcd.tcl. So I was wondering if sscache can be utililized
for secondary structure determination of the large dcd file aong with
the bigdcd script. Any view on this would be really helpful.

Thanks
Puspita

On 6/26/14, Jeremiah Babcock <zhc605_at_my.utsa.edu> wrote:
> Hi Puspita,
> Not sure if you did this but if you just need the secondary structure
> of the protein you could strip out the solvent molecules. That would really
> help on the file size. Also, which OS version are you using?
>
> Regards,
> Jeremiah Babcock
>
>
> On Wed, Jun 25, 2014 at 8:23 AM, Puspita Halder <puspitah_at_gmail.com> wrote:
>
>> Dear VMD users,
>>
>> I need to generate the secondary structure of my protein from a 50 ns
>> simulation run. I used sscache earlier for 2-4 ns simulations of the
>> protein. Now the file sizes are huge (~ 50 GB) so I assume that I cannot
>> directly use sscache. I tried to combine sscache with bigdcd.tcl script
>> but
>> failed to do so. Please help me with your valuable suggestions regarding
>> this. Is there any ready script available ?
>>
>> Thanks
>> Puspita
>>
>