You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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.
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, ***@***.***> 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
<#30 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AOYQZJDE5W7ND225YCM6Q6LTA2NLRANCNFSM4VKDDYEA>
.
chap -f 7_4.xtc -s new.tpr
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)
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!
The text was updated successfully, but these errors were encountered: