Help wanted: Using lipid_elastic_properties and align_trajectory with Martini output

[nambiarnik]

I wanted help in converting the gromacs output files for Martini systems to get the .dcd and .pdb files needed for these modules. I was able to run the example scripts (hex_phase) in ost by importing the module, but all my attempts at using a converted trajectory .dcd file is giving me errors. Could you give me any insight on how this could be run.

[reneejiang]

Hi, I think you can use PARMED in Amber, which can use the function "gromber" to change a gromacs pdb and top to an amber rst7 and parm7, make sure the input gromacs pdb is using PBC MOL structure. And then you can try to read in parm7 and read xtc file to convert to a DCD file. hope it helps. Best Wenjuan

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On Wed, May 6, 2020 at 8:45 AM nambiarnik ***@***.***> wrote: I wanted help in converting the gromacs output files for Martini systems to get the .dcd and .pdb files needed for these modules. I was able to run the example scripts (hex_phase) in ost by importing the module, but all my attempts at using a converted trajectory .dcd file is giving me errors. Could you give me any insight on how this could be run. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVWVZGGKVU33GLCUVOUQFDRQGAYTANCNFSM4M2RYKHA> .

-- Best regards Wenjuan Jiang

[njohner]

This is too little information if you want help.

• What error did you get? what is the traceback?
• How did you do the conversion from gromacs?
• What does your pdb? Could you load your converted PDB and DCD in some visualization software like VMD? did it look OK, or did something go wrong with the conversion?

From the top of my head (I don't work in the field anymore since several years), I think for example that the masses are needed in the PDB file. Are they present?

[marleysamways]

I may have run into a similar issue recently, which turned out to be caused by the simulation cell angles not being read in correctly from the DCD. I resolved this by converting the XTC->DCD using mdtraj, and then it seemed to work, if that's any help...