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.cpptraj
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/>
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- application/octet-stream attachment: pca.in
Received on Wed Mar 15 2017 - 10:00:02 PDT
