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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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Dec 14 2016 - 03:00:03 PST
