Great I did not know that chimera has that option I will check both output and see if there is any difference
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: David Sáez <davidsaez.udec.cl>
Sent: Tuesday, March 31, 2020 8:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] checkstructure with cpptraj
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Hi,
As Gustaf, Daniel and Ahmed pointed out, you input must be:
parm parm_water.Parm7 #Load topology
trajin Heating.nc #Load the trajectory/coordinates checkstructure #Check overlap
Besides CPPTRAJ, you can check overlaps visually with Chimera (Tools>Structure Analysis> Find Clashes/Contacts).
regards.
On Sun, Mar 29, 2020 at 8:18 PM Nicolas Feldman <nfeldman01.qub.ac.uk>
wrote:
> 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
>
> This message is from an external sender. Please take care when
> responding, clicking links or opening attachments.
>
> 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 Tue Mar 31 2020 - 13:30:02 PDT
