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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
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terminal protonation state modification #362

Closed WangLiguo-kyrie closed 4 months ago

WangLiguo-kyrie commented 4 months ago

When I use the polyply to generate protein topol based on the ff file (even the aminoacids.ff of standard M3) in working dir, polyply can't recognize the ternimal protonation state, as default P2 backbone was genrated for ternimus. But if I use -lib martini3 option, the ternimus would be Q5.

Polyply version: 1.5.0 and 1.6.1

Command line arguments polyply gen_params -name WGR5PRT -f aminoacids.ff -seqf WGR5.fasta -o WGR5PRT.itp

fgrunewald commented 4 months ago

What do you mean by 'aminoacids.ff of standard M3' ? Note that the termini in polyply are always charged by default and that the ff file is not the same as in vermouth.

WangLiguo-kyrie commented 4 months ago

Okay, I see. Right, the terminal protonation description in vermouth ff file is not totally the same with that in Polyply. I just used the vermouth file. Now I change the terminal protonation according to polyply format, it works!