On 2013-06-26 09:14, hamid mosaddeghi wrote:
Dear David
thansk for quick reply, but existed one problem, my system include metal
and protein that metal not define in gromacs then writing topology is
difficult, how do analysis with gromacs without write toplogy?
any suggestion will be appreciated
for some analysis you do not need it at all. For some analysis you could
also leave out the metal (e.g. secondary structure of protein).
----- Forwarded Message -----
*From:* David van der Spoel <sp...@xray.bmc.uu.se>
*To:* gmx-users@gromacs.org
*Sent:* Wednesday, 26 June 2013, 11:10
*Subject:* Re: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-25 21:52, hamid mosaddeghi wrote:
> Dear all
>
> I did some bio simulation by dl_poly ,is it possible use gromacs for
analysis data?
>
>
> Best Of Luck
>
sure,if you can output the sim as e.g. a pdb file with multiple
frames/models. Some analysis tools need a gromacs topology file which is
easy to make for proteins/nucleic acids. Run a gromacs tutorial if you
haven't yet.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> http://folding.bmc.uu.se/
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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