Hi,
I tried with vmd as suggested.
Since snapshot has no no water, I use the prmtop without water or ions
(the same file i used without any problem in mmpbsa and all others)
but it didnt work with snapshots. its not getting visualized. The
error is:
xyz structure) missing type or coordinate(s) in file
'/md/md_at4g/snaps/at4g_com.crd' for atom '402'
ERROR) Error reading optional structure information from coordinate
file /md/md_at4g/snaps/at4g_com.crd
ERROR) Will ignore structure information in this file.
Info) Using plugin xyz for coordinates from file /md/md_at4g/snaps/at4g_com.crd
Info) Finished with coordinate file /md/md_at4g/snaps/at4g_com.crd
Are u familiar with such errors?
I tried with many other snapshots from different systems also.
Thanking you
mary
On 12/14/16, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
> Yes,
> You can use VMD to visualize.
> Load your prmtop file and the XYZ.crd file.
>
>
> Regards
>
> *Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
> [image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
> Website: http://www.elvismartis.in <http://www.elvismartis.in/>
> group website: http://www.profeccoutinho.net.in/
> Address:
>
> Kalina, Santa Cruz [E]
> , Mumbai, 400 098, INDIA
>
> Alt. e-mail: emartis12.live.com
> <https://in.linkedin.com/in/elvisadrianmartis>
>
>
> On 14 December 2016 at 13:48, Mary Varughese <maryvj1985.gmail.com> wrote:
>
>> [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
>> for Automatic Cleanup! (maryvj1985.gmail.com) Add cleanup rule
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>>
>> Sir
>>
>> Is there any way to visualize the snapshots generated in mmpbsa
>> calculation (.crd files).
>>
>>
>>
>> mary varughese
>>
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Received on Wed Dec 14 2016 - 02:00:02 PST
