convert amber trajectory to desmond compatible (cms with trj)

[amrhamedp]

Hello,
I would like to convert amber trajectory to desmond compatible one to make use of simulation interaction analysis found in desmond.....any clue how to do this?

[rmcgibbo]

MDTraj does not have this capability.

…

On Wed, May 10, 2017 at 12:54 PM, amrhamedp ***@***.***> wrote: Hello, I would like to convert amber trajectory to desmond compatible one to make use of simulation interaction analysis found in desmond.....any clue how to do this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1261>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAnI_oEcIS6-ZvzmOLbDBYH_gmsz5PxBks5r4evTgaJpZM4NW8fu> .

-- -Robert

[peastman]

What formats does Desmond support? It would be kind of surprising if it can't read a few standard formats like PDB and DCD, in addition to its own proprietary formats.

[mpharrigan]

I think we can save dtr, isn't that the desmond format?

[amrhamedp]

what I am really looking for is to use simulation interaction analysis in desmond:
http://content.schrodinger.com/Resources/SID/3p6h_desmond_npt_10ns.pdf
This tool in the GUI form accepts cms file (which point to trj file) only. I don't know if there is a way around to read a pdb trajectory file. I don't know even if this tool can be run using command line.
Any suggestion to an equivalent tool that can analyze ligand protein interactions of a given trajectory while showing the percentage of each interaction and whether it is water mediated or not is welcomed

[amrhamedp]

Ok I figured this out....it needs careful translation of atom types to desmond and vmd

[yefei111]

Ok I figured this out....it needs careful translation of atom types to desmond and vmd

Hi, could you please share the methods for trajectory translation? Thank you very much!
My MD simulation was performed by gromacs. I have transfered the .xtc trajectory to desmond trajectory file. Then, we generated the .cms file according to this protocol (https://www.schrodinger.com/kb/989). I can read the cms and trajectory file in SCHRODINGE GUI. However, when I performed Simulation Interactions Diagram, there came this error:
Traceback (most recent call last):
File "analyze_trajectories.py", line 181, in
run()
File "analyze_trajectories.py", line 175, in run
main(cmsfn, st2fn, outfn, trjfn=options.trj_fn, cfgfn=options.cfg_fn)
File "/.../SCHRODINGER/mmshare-v30010/lib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/trajectory/analyze_trajectories.py", line 1116, in main
if _KeywordProcessor.requires_energy(ark["Keywords"]):
File "/.../SCHRODINGER/mmshare-v30010/lib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/trajectory/analyze_trajectories.py", line 173, in requires_energy
for kw in ark_kws:
TypeError: 'Atom' object is not iterable

Do you have any clues to deal with it? Thank you!

[bio-hpc]

Ok I figured this out....it needs careful translation of atom types to desmond and vmd

Hi, could you please share the methods for trajectory translation? Thank you very much! My MD simulation was performed by gromacs. I have transfered the .xtc trajectory to desmond trajectory file. Then, we generated the .cms file according to this protocol (https://www.schrodinger.com/kb/989). I can read the cms and trajectory file in SCHRODINGE GUI. However, when I performed Simulation Interactions Diagram, there came this error: Traceback (most recent call last): File "analyze_trajectories.py", line 181, in run() File "analyze_trajectories.py", line 175, in run main(cmsfn, st2fn, outfn, trjfn=options.trj_fn, cfgfn=options.cfg_fn) File "/.../SCHRODINGER/mmshare-v30010/lib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/trajectory/analyze_trajectories.py", line 1116, in main if _KeywordProcessor.requires_energy(ark["Keywords"]): File "/.../SCHRODINGER/mmshare-v30010/lib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/trajectory/analyze_trajectories.py", line 173, in requires_energy for kw in ark_kws: TypeError: 'Atom' object is not iterable

Do you have any clues to deal with it? Thank you!

Our group try to convert Gromacs to Desmond and we need to obtain the cms file. Do you get a solution to do this? Thanks

[NaveenKumar56]

@yefei111 Hi. I am facing similar problem and only getting cms file and it is not working properly in maestro. I couldn't play trajectory file. I am also not sure that the way I am converting .xtc files into cms file properly. Can you please share how you actually did it.