cpptraj will allow you to specify a different prmtop and
reference coordinate set when doing RMSD calculations... it can get
complicated if atoms don't match up, but your case sounds like a single
atom mask will give the same selection for both systems so it should work
smoothly. Dan Roe or others might have more detailed advice, but this works
for me.
I use something like this in my cpptraj script.
load both prmtops, with a label for the alternate one
parm ./prmtop
parm ../build_40/prmtop [refparm]
define reference structures, indicating the alternate prmtop for the other
system, and label each reference structure for use later:
reference ./1min.rst7 [refinit]
reference ../build_40/struct40.rst7 parm [refparm] ref [ref40]
trajin ./md.x
calculate rmsd to the SAME system:
rmsd rms1 :
10-70.CA,N,C,O out rmsd.10-70.dat ref [refinit]
and then when doing the rmsd to the alternate system:
rmsd rms2 :
10-70.CA,N,C,O out rmsd.10-70.ref40.dat ref [ref40]
On Fri, Oct 2, 2020 at 10:56 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> 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
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 02 2020 - 08:30:02 PDT
