Fw: [gmx-users] ***using output of dl_poly in gromacs??***
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 26 09:42:33 CEST 2013
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 <spoel at xray.bmc.uu.se>
> *To:* gmx-users at 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.
> spoel at xray.bmc.uu.se <mailto:spoel at 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.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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