Hi Shahab,
As Jason suggested, goggling this problems turns up a lot of useful information, which is how I found this way, that works for me.
Please note that this information took me a while to figure out by trial and error, so for the future, people are more helpful if you show that you have tried to solve a problem yourself first.
1) Create a "fake" .tpr file to work with "grompp".
For this you need a .top file. It is a good exercise to make your own .top file so you know which information goes where, and how the force fields are handled in different programs.
If you your confident you know what is going on, you can use VMD to create a "fake" .top file. Notice that both the .top and the .tpr file are not working files to ever be used in simulations. They only contain a limited set of information in order to run the gromas analysis programs!
To create the .top file you need to get the VMD plugin "Topotools". When you have it, run the following commands in the TkConsole:
package require Topotools
topo writegmxtop <filename>.top
When you have your fake .top file, find yourself a .mdp file. Again, google is your friend.
Be aware that the .mdp file needs to have temperature coupling groups, energy groups etc. that makes sense in accordance with your system!
Run grommp, for instance like this: (NB: you need box info to be present in the .pdb file)
grompp -f <your mdp file>.mdp -c <your pdb file>.pdb -p <your top file>.top -o <your tpr file>.tpr
If needed, you can set "maxwarn" to a desired number.
2) Convert your amber trajectory into a gromacs format trajectory:
For this you need the amber program "trjconv" together with VMD. trjconv is able to read amber trajectories via VMD, rather neat.
The thing to know here is, that if you run a 64-bit version of VMD your gromacs installation needs to be 64-bit as well - the same goes for 32-bit.
Also, the file extension for your amber trajectory needs to be written as VMD expects it - i.e. ".netcdf" and not for instance ".nc"
trjconv -f <your amber trajectory>.netcdf -s <your tpr file>.tpr -o <your gromacs trajectory>.trr (or .xtc if you want a more compact format) - time <number of ps per frame>
And then your good to go :-)
Best,
Sarah
Den 26/12/2014 kl. 16.07 skrev Jason Swails <jason.swails.gmail.com>
:
> I googled "Convert Amber topology to Gromacs" and came up with this:
> http://www.gromacs.org/Downloads/User_contributions/Other_software
>
> This question is more appropriate for the Gromacs forums or email list.
> Amber developers are unlikely to choose gromacs programs for analysis
> compared to cpptraj, so there is no reason that we would know about tools
> like these better than Gromacs developers/users.
>
> HTH,
> Jason
>
> On Fri, Dec 26, 2014 at 8:16 AM, shahab shariati <shahab.shariati.gmail.com>
> wrote:
>
>> Dear Kshatresh
>>
>> Thanks for your answer.
>>
>> VMD is only suitable for trajectory converting ( mdcrd to trr file).
>>
>> Also, I need to convert topology ( prmtop to top file).
>>
>> Have not you idea about topology conversion?
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Dec 26 2014 - 16:30:02 PST
