How write TPR files

[Ropon-Palacios G.]

Dear user,

 

I’m try write TPR file from DCD and PSF file of NAMD simulation.

 

Please suggest me and example for write this.

 

Best,

 

Geo.

[Irfan Alibay]

Hi,

MDAnalysis does not handle the direct writing of TPR files unfortunately.

I assume that something like InterMol (https://github.com/shirtsgroup/InterMol) or ParmEd (https://github.com/ParmEd/ParmEd) would have to be used to generate itp/gro files from DCD/PSF inputs.

I'll let others who are more familiar with CHARMM -> GROMACS conversions take over here (it's not something I have had to do before outside of CHARMM-GUI).

Best regards,

Irfan

[Ropon-Palacios G.]

Dear them,

 

MDanalysis have any algorithm for perform clustering of structures , for example I like perform clustering of proteins based into binding site from NAMD trajectories, it is possible into MDanalysis?, Too write into pdb file representative clusters?  

 

Best,

 

Geo.

--
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to mdnalysis-discus...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/cbf4daba-276a-45bc-8724-b4e4726f98a8n%40googlegroups.com.