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marrink-lab / polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Apache License 2.0
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"Segmentation fault" with polyply gen_coords #288

Closed Romumrn closed 1 year ago

Romumrn commented 1 year ago

Hi Fabian, I have a problem when I want to pegylate a protein. I have a "Segmentation fault (core dumped)" issue during the generating system coordinates step. Please can you help me with this problem ?

So this is my command line :

polyply gen_coords -p system.top -o out.gro -name protPEG -c coord.gro -box 15 15 15

And my files :

coord.gro polymere.itp system.top

Thank you in advance for your help :)

Romu

fgrunewald commented 1 year ago

Hi @Romumrn

The issue is for sure that there are two nan coordinates in your .gro file. We should probably raise an error but that's more a vermouth than polyply issue as the parser is in vermouth.

Romumrn commented 1 year ago

Thank you for your fast reply ! I remove the nan values and everything works well now !