Dear Amber developers and users,
I have two structures identical except for a difference in co-factor charge.
Thus one has a Cl- ion extra added by tleap, but the number of
protein, non-standard residue and water atoms are identical.
Now, how do I compare the rmsd of the two trajectories snapshot by snapshot?
Both trajectories start from the same PDB, thus I want to check if (how
much) there is a divergence in the coordinate-space that they sample as
they move along the MD trajectories.
Is it possible/meaningful to compare reorganization of waters and AA
between the two trajectories w.r.t. to coordinates and energies? As
suggested earlier I will try to use imin=5 for this, but first I think I
need to resolve incompatibility due to the extra Cl- ion. Both Cl-s are >
10 A from cofactor, so is it safe to simply ignore them and delete from
both prmtop before rmds or other analysis?
I tried to use cpptraj to estimate rmsd for one trajectory using prmtop of
another which failed (then realized the small but important difference
between the two).
Is it possible to simply delete the extra/both Cl- from prmtop with parmed
and will it then work with cpptraj for all kinds of analysis.
Please suggest.
Looking forward to valuable suggestions from the list on this.
thank you and best regards.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Fri Oct 02 2020 - 08:00:02 PDT
