Hello Dan,
Thanks a ton.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Wednesday, March 15, 2017 10:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] About PCA with cpptraj
COORDS data sets need to correspond to one topology. The easy solution (and one that will use less memory) is to strip everything outside the mask you're using, :1-316.CA,C,N,O,H, so that each input trajectory has the same number of atoms. So add this somewhere before your 'createcrd' command:
strip !(:1-316.CA,C,N,O,H)
Also, you probably want to change 'run' to 'runanalysis' after all of your 'hist' commands since at that point you're really not interested in analyzing your 'trajin' trajectories (everything is in your COORDS set at that point).
-Dan
On Wed, Mar 15, 2017 at 12:34 PM, Elvis Martis <elvis.martis.bcp.edu.in> wrote:
> Hello,
> I am trying to perform a Principal Component Analysis to understand the changes in the internal dynamics of an enzyme when two different ligands bind.
>>> 1) When ADP (substrate) binds there is an Mg2+ present in the
>>> vicinity, hence size of system becomes 318 residues (= 316 AA + 1
>>> ion + I ligand)
>>> 2) When the inhibitor binds there is not Mg2+ present and hence size
>>> of the becomes 317 residues (=316 AA + 1 ligand)
> I am interested particularly in knowing how the backbone dynamics changes.
> I have performed 3 independent productions runs for each complex, leading to a total of 6 trajectories with 10000 snapshots each. For analysis I ignore the first 1000 snapshots.
> While performing PCA I pool all the trajectories together with script
> attached (pca.in) along with this mail. >> Hence I am following the
> tutorial script which I modified for my case
> http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/pca-cpu-gpu.c
> pptraj Cpptraj correctly understands that there are in total 54000
> snapshots, however when I try to create coordinate dataset using the
> following command "Createcrd ALL-trajectories" >>> line 11 in the
> attached file (pca.in) The following error is displayed "[createcrd
> ALL-trajectories]
> Error: # atoms in current topology (5118) != # atoms in coords set
> "ALL-trajectories" (5121)
> Error: Setup failed for [createcrd]
> Warning: Could not set up actions for compl_dry.prmtop: skipping.
> Read 27000 frames and processed 27000 frames."
> Here, I understand that cpptraj is not reading the frames from 27001 to last (i.e. 54000).
> I have also attached the cpptaj.log that displays step-by-step action taken by cpptraj until the error comes.
> FYI: I am using cpptraj v16.16
>
> Please help me resolve this.
> Thank you in advance.
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
>
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Mar 15 2017 - 10:30:03 PDT
