Fw: [gmx-users] ***using output of dl_poly in gromacs??***

[David van der Spoel]

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