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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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some error about dssp #562

Closed bdx114514 closed 7 months ago

bdx114514 commented 7 months ago

Hello,

I use "martinize2 -f B2A31.pdb -x B2A3_CG.pdb -ss B2A31.dssp -ff martini3001 -o topol.top" to generate CG and top file, but it shows the following error: ValueError: The length of the sequence (10) does not match the number of residues in the selection (180).

If I change to use "martinize2 -f B2A31.pdb -x B2A3_CG.pdb -dssp mkdssp -ff martini3001 -o topol.top ", It shows: Error trying to load file "/home/yancong/Desktop/MD11_26/dssp_in_670i2c0g.pdb" Expected record CRYST1 but found ATOM
. The input file provided to DSSP can be found at /home/yancong/Desktop/MD11_26/dssp_in_670i2c0g.pdb. It seems that there is a temporary file named dssp_in_670i2c0g.pdb that has not been generated correctly, and a line “CRYST1” is missing files.zip I have uploaded all the relevant files.

pckroon commented 7 months ago

Hellohello,

which version of martinize2 are you using? Which version of dssp are you using? We're unfortunately limited to versions (if memory serves) 2 and 3. You can try the branch from PR #547, which uses dssp from the mdtraj library

bdx114514 commented 7 months ago

Reference in

I used the latest version of DSSP (4.0) before, but now I switched to an older version (3.0.10), and there are no errors now. Thanks!