normal Viewing MARTINI models with CONECT records

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3 years 8 months ago #8644 by darrenphua
Viewing MARTINI models with CONECT records was created by darrenphua
I am aware that using gmx trjconv once mdrun is completed would be able to show martini models with connecting bonds. This is done by input of -conect.

However, if i want to view the connecting bonds in a martini model immediately after converting the all-atom model to martini, can this be done using gmx editconf? I see from the documentation that editconf has a -conect option, but i received this error in doing so.

Assertion failed:
Condition: fio->xdr != nullptr
Implementation error: NULL XDR pointers


The command line i input is this:
gmx editconf -f protein-CG.pdb -o protein-CG-conect.pdb -conect

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3 years 7 months ago #8656 by peterkroon
Replied by peterkroon on topic Viewing MARTINI models with CONECT records
You need to give editconf a tpr file, since that contains the necessary information. You can create a minimization tpr (without actually running the minimization) for this purpose.

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