Hi,
It worked. Thank you very much sir.
mary
On 12/14/16, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
> Hi,
> What extension did you choose to lead your coordinate file, i.e., crd file?
> Select file type as "AMBER RESTART" and not AMBER coordinates or AMBER
> coordinates with Periodic BOX.
> Sorr, I forgot to mention this.
>
> 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 15:21, Mary Varughese <maryvj1985.gmail.com> wrote:
>
>> [image: Boxbe] <https://www.boxbe.com/overview> Automatic Cleanup: keep
>> last 3 emails (maryvj1985.gmail.com) Edit rule
>> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3D2i8Hp2Q2Dmi4WnVQwXRQpgyLIhF3ZvSZ2ws%252FRNDejwo%253D%26token%3D%252FPk29XnP%252BvyESOCNWqAeNB%252BG3YYM6GKlVZRtp29WxdXhAgE%252BYQUaxgdZmmKnvLRtbBUFnVWhYWdqcxCKUrRbYY2k4UG70BFFF%252F8ympOBtawUFiRDHl%252BDSVHmuIHL%252BbcIRkYrljqTV%252BE%253D&tc_serial=27995952650&tc_rand=548281326&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_EDIT&utm_content=001>
>> | Delete rule
>> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3D2i8Hp2Q2Dmi4WnVQwXRQpgyLIhF3ZvSZ2ws%252FRNDejwo%253D%26token%3D%252FPk29XnP%252BvyESOCNWqAeNB%252BG3YYM6GKlVZRtp29WxdXhAgE%252BYQUaxgdZmmKnvLRtbBUFnVWhYWdqcxCKUrRbYY2k4UG70BFFF%252F8ympOBtawUFiRDHl%252BDSVHmuIHL%252BbcIRkYrljqTV%252BE%253D&tc_serial=27995952650&tc_rand=548281326&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_EDIT&utm_content=001>
>> | Mark important
>> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3D2i8Hp2Q2Dmi4WnVQwXRQpgyLIhF3ZvSZ2ws%252FRNDejwo%253D%26token%3D%252FPk29XnP%252BvyESOCNWqAeNB%252BG3YYM6GKlVZRtp29WxdXhAgE%252BYQUaxgdZmmKnvLRtbBUFnVWhYWdqcxCKUrRbYY2k4UG70BFFF%252F8ympOBtawUFiRDHl%252BDSVHmuIHL%252BbcIRkYrljqTV%252BE%253D%26important%3Dtrue%26emlId%3D53810182108&tc_serial=27995952650&tc_rand=548281326&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_EDIT&utm_content=001>
>>
>> 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
>> >> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.
>> com%2Fcleanup%3Fkey%3DWWOimqPPPzRBetYIjHhxuOiaoqUW
>> 10O6fekD%252BRgw2Mk%253D%26token%3DNVD%252B6u7CMBEoeThz8bl5rRYIHNbmp4
>> PVtclzb%252FwLqYDp378NArM0fDpRQA%252BGxmvehVS0RjUJK3dU2faz00xFfwwLfzoaDc%
>> 252FQgEQtpppSoAH5Pslksjyb2%252BSB%252FE%252FKlGFB%
>> 252Bla1QRFO3lQ%253D&tc_serial=27994319643&tc_rand=
>> 1368608390&utm_source=stf&utm_medium=email&utm_campaign=
>> ANNO_CLEANUP_ADD&utm_content=001>
>> >> | More info
>> >> <http://blog.boxbe.com/general/boxbe-automatic-
>> cleanup?tc_serial=27994319643&tc_rand=1368608390&utm_source=
>> stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>> >>
>> >> Sir
>> >>
>> >> Is there any way to visualize the snapshots generated in mmpbsa
>> >> calculation (.crd files).
>> >>
>> >>
>> >>
>> >> mary varughese
>> >>
>> >> _______________________________________________
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>> >>
>> >>
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>> >
>>
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>>
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Received on Wed Dec 14 2016 - 03:00:04 PST
