That is correct.
I think the problem might be that both structures are solvated. Since 1d7p is slightly bigger the amount of solvent atoms might differ.
________________________________________
Von: Daniel Roe <daniel.r.roe.gmail.com>
Gesendet: Montag, 23. April 2018 15:30:48
An: AMBER Mailing List
Betreff: Re: [AMBER] average between structures with different residue numbering
Hi,
Which topology is the one with 3 extra residues? I assumed it was 1d7p
- is that correct?
-Dan
On Mon, Apr 23, 2018 at 10:22 AM, Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
> 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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>
> _______________________________________________
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> 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 - 08:00:02 PDT
