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channotation / chap

CHAP is a tool for the functional annotation of ion channel structures:
http://www.channotation.org
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error in pore path recognition. #30

Open Y0geshh opened 3 years ago

Y0geshh commented 3 years ago

chap -f 7_4.xtc -s new.tpr

             CCCCCC  HH     HH    AAA    PPPPPPPP
            CC    CC HH     HH   AA AA   PP     PP
            CC       HH     HH  AA   AA  PP     PP
            CC       HHHHHHHHH AA     AA PPPPPPPP
            CC       HH     HH AAAAAAAAA PP
            CC    CC HH     HH AA     AA PP
             CCCCCC  HH     HH AA     AA PP

         The Channel Annotation Package, version 0.9.1

Reading file new.tpr, VERSION 2018 (single precision) Reading file new.tpr, VERSION 2018 (single precision) Available static index groups: Group 0 "System" (47651 atoms) Group 1 "Protein" (3533 atoms) Group 2 "Protein-H" (1752 atoms) Group 3 "C-alpha" (236 atoms) Group 4 "Backbone" (708 atoms) Group 5 "MainChain" (944 atoms) Group 6 "MainChain+Cb" (1148 atoms) Group 7 "MainChain+H" (1169 atoms) Group 8 "SideChain" (2364 atoms) Group 9 "SideChain-H" (808 atoms) Group 10 "Prot-Masses" (3533 atoms) Group 11 "non-Protein" (44118 atoms) Group 12 "Other" (44118 atoms) Group 13 "POPC" (17420 atoms) Group 14 "POT" (23 atoms) Group 15 "CLA" (26 atoms) Group 16 "TIP3" (26649 atoms) Specify a selection for option 'sel-pathway' (Reference group that defines the permeation pathway (usually 'Protein') ): (one per line, for status/groups, 'help' for help)

1 Selection '1' parsed

Reading frame 500 time 5000.000

Program: chap, version 2018

Standard library runtime error (possible bug): (exception type: St13runtime_error) Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff.

For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors

Thank you for using CHAP - The Channel Annotation Package!

Inniag commented 3 years ago

Have you tried the suggestion:

Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff.

Y0geshh commented 3 years ago

Hi Channotation/Chap Can you please provide an example cut off file. I tried to give manual pore coordinates to keep probe radius. But I don't know why it keeps happening. Chap can hardly read trajectory of about 40ns. It terminates with the same error again. Even when there is an obvious single channel in transmembrane protein.

On Fri, 26 Feb, 2021, 12:34 am Inniag, notifications@github.com wrote:

Have you tried the suggestion:

Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/channotation/chap/issues/30#issuecomment-786131637, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOYQZJDE5W7ND225YCM6Q6LTA2NLRANCNFSM4VKDDYEA .