[AMBER] checkstructure with cpptraj

From: Nicolas Feldman <nfeldman01.qub.ac.uk>
Date: Sun, 29 Mar 2020 15:26:34 +0000

Hello I'm trying to check if there is any clash between aminoacid using CPPTRAJ, but when I run the checkstructure function I got:
Warning: Action specified before trajin/ensemble. Assuming trajin.
CHECKSTRUCTURE: Checking atoms in mask '*', warnings output to STDOUT.
Number of problems in each frame will be saved to set 'CHECK_00001'
 Checking for bond lengths > Req + 1.15 Ang
Checking for inter-atomic distances < 0.80 Ang.
Cutoff for building pair list is 4.000000 Ang.

Do I have to set the protein before loading it to CPPTRAJ ? it is save as .parm7

Thank you in advance

Nicolas Feldman
PhD Student
The Wellcome-Wolfson Institute for Experimental Medicine
Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL

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Received on Sun Mar 29 2020 - 08:30:01 PDT
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