Hi Gustaf,
No worries at all.
It was not a video effect, I had a restriction of some water molecules. Probably because I did not understand quiet a the parameters when writing the input files.
My idea is to prepare the molecule before running the minimization/equilibrium. I saw some people that used swisspro to saw amino acid clash. But I'm using VMD and because I saw that some people use CPPTRAJ, I could may be give it a chance.
But if there is any other way to see this in any amber MD I don't may using it.
Nicolas Feldman
PhD Student
The Wellcome-Wolfson Institute for Experimental Medicine
Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
-----Original Message-----
From: Gustaf Olsson <gustaf.olsson.lnu.se>
Sent: Sunday, March 29, 2020 8:47 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] checkstructure with cpptraj
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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 <nfeldman01.qub.ac.uk>
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 - 16:30:02 PDT
