hi Dan,
thanks for the help. I tried your code but I get an error with the line:
trajin part2.nc parm [1iqd]
Reading 'part2.nc' as Amber NetCDF
Error: Number of atoms in NetCDF file part2.nc (54055) does not
Error: match number in associated parmtop (54511)!
Error: Could not set up part2.nc for reading.
Error: Could not set up input trajectory 'part2.nc'.
best
Martin
________________________________________
Von: Daniel Roe <daniel.r.roe.gmail.com>
Gesendet: Montag, 23. April 2018 14:43:24
An: AMBER Mailing List
Betreff: Re: [AMBER] average between structures with different residue numbering
Hi,
What I would do is strip away all the stuff I don't want from the
second trajectory, combine with first, then average that. Note that
you probably want to remove global translation/rotation when
generating your average structure, so add an RMS-fit in there as well.
So e.g.
parm 1iqd/WT.prmtop [1iqd]
parm 1d7p/WT.prmtop [1d7p]
# Strip 1-3 from second traj
trajin 1d7p/WT.inpcrd parm [1d7p]
strip :1-3
trajout part2.nc parm [1d7p]
run
clear trajin
# Combine with first and average
trajin 1iqd/WT.inpcrd parm [1iqd]
trajin part2.nc parm [1iqd]
rms first .CA
average 1iqd_1d7p_avrg.pdb .CA
Hope this helps,
-Dan
On Mon, Apr 23, 2018 at 7:31 AM, Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
> Hi,
>
> for a PCA I am trying to calculate the average between the unbound C2 domain of factor VIII (https://www.rcsb.org/structure/1d7p) and the bound C2 domain extracted from https://www.rcsb.org/structure/1iqd .
>
> My problem is that the unbound C2 domain has 3 additional residues at the beginning. After simulation, residue numbers run from 1-159 whereas the extracted unbound structure has the numbering 1-156.
>
> When I calculate the average over the two structures it seems like the wrong residues are matched.
>
> parm 1iqd/WT.prmtop [1iqd]
> parm 1d7p/WT.prmtop [1d7p]
> trajin 1iqd/WT.inpcrd parm [1iqd]
> trajin 1d7p/WT.inpcrd parm [1d7p]
> average 1iqd_1d7p_avrg.pdb .CA
>
> How can I tell cpptraj that I want to match residues 4-159 with 1-156?
> _______________________________________________
> 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 Mon Apr 23 2018 - 07:30:02 PDT
