Re: [AMBER] checkstructure with cpptraj

From: Gustaf Olsson <>
Date: Sun, 29 Mar 2020 19:47:08 +0000

Hello Nicolas

Sorry for the late, and now short reply. I saw your video and it looks like you are indeed doing MD simulations. Congratulations, don't know if this was an "video effect" or if you had some restraints affecting some of the water molecules though some seemed quite stationary.

I have not used this feature of cpptraj before though the general order is loading the prmtop file, then trajin loading the coordinate files. Then supplying the action to take.

Is this a file you are preparing to use for MD simulations or is this checking the output after an initial minimization/equillibration?

// Gustaf

Från: Nicolas Feldman <>
Skickat: den 29 mars 2020 17:26:34
Till: AMBER Mailing List
Ämne: [AMBER] checkstructure with cpptraj

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 - 13:00:02 PDT
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