normal Alternative positions in martinize2 script giving errors

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11 months 2 weeks ago #8290 by andreashlarsen
Hi Martini developers,

I experienced a problem with martinize2 (martinize with vermouth 0.1.1.dev2), for a protein with this His residue:

ATOM 1298 N AHIS A 194 -12.445 -22.119 70.350 0.56 53.73 N
ATOM 1299 N BHIS A 194 -12.456 -22.138 70.361 0.44 53.63 N
ATOM 1300 CA AHIS A 194 -13.902 -22.133 70.272 0.56 53.66 C
ATOM 1301 CA BHIS A 194 -13.910 -22.208 70.255 0.44 53.81 C
ATOM 1302 C AHIS A 194 -14.412 -22.078 68.838 0.56 55.48 C
ATOM 1303 C BHIS A 194 -14.397 -22.147 68.813 0.44 55.40 C
ATOM 1304 O AHIS A 194 -15.551 -22.481 68.579 0.56 58.40 O
ATOM 1305 O BHIS A 194 -15.510 -22.602 68.527 0.44 58.29 O
ATOM 1306 CB AHIS A 194 -14.458 -20.961 71.097 0.56 56.02 C
ATOM 1307 CB BHIS A 194 -14.557 -21.082 71.069 0.44 55.99 C
ATOM 1308 CG AHIS A 194 -15.936 -20.757 70.964 0.56 55.18 C
ATOM 1309 CG BHIS A 194 -14.766 -21.421 72.512 0.44 56.47 C
ATOM 1310 CD2AHIS A 194 -16.664 -19.635 70.748 0.56 55.89 C
ATOM 1311 ND1AHIS A 194 -16.845 -21.788 71.067 0.56 54.97 N
ATOM 1312 CD2BHIS A 194 -15.012 -22.604 73.123 0.44 55.97 C
ATOM 1313 ND1BHIS A 194 -14.736 -20.473 73.513 0.44 57.34 N
ATOM 1314 CE1AHIS A 194 -18.067 -21.314 70.906 0.56 54.23 C
ATOM 1315 NE2AHIS A 194 -17.986 -20.010 70.712 0.56 54.74 N
ATOM 1316 CE1BHIS A 194 -14.953 -21.058 74.678 0.44 56.35 C
ATOM 1317 NE2BHIS A 194 -15.121 -22.351 74.469 0.44 56.59 N

I got the error:
KeyError: 'Could not identify PTM'

it worked after I removed the alternative B atoms.

might be nice, e.g. to use alternative atom A and throw a warning...?

Cheers,
Andreas

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11 months 2 weeks ago #8291 by peterkroon
Hi Andreas,

thanks for the feedback! We'll definitely look into it. We'll probably make it a commandline option to select a model.

(I'd swear we already did this, but apparently I'm mistaken)

Peter

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11 months 2 weeks ago #8292 by andreashlarsen
thank you. I just tried to download the newest version from github (martinize with vermouth 0.2.0), and get the same error...

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11 months 2 weeks ago #8296 by peterkroon
Correct :)
It should be fixed in PR211 [1], in case you're feeling adventurous.

[1] github.com/marrink-lab/vermouth-martinize/pull/211

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