thanks again.
Interestingly after stripping water, ions and the 3 residues the two structures still differed by 3 atoms. Removing hydrogen as well solved the issue.
cheers
Martin
________________________________________
Von: Daniel Roe <daniel.r.roe.gmail.com>
Gesendet: Montag, 23. April 2018 15:58:19
An: AMBER Mailing List
Betreff: Re: [AMBER] average between structures with different residue numbering
Oh, in that case strip out all the water as well:
parm 1iqd/WT.prmtop [1iqd]
parm 1d7p/WT.prmtop [1d7p]
# Strip water from first traj
trajin 1iqd/WT.inpcrd parm [1iqd]
strip :WAT parmout part1.parm7
trajout part1.nc parm [1iqd]
run
clear trajin
# Strip water and 1-3 from second traj
trajin 1d7p/WT.inpcrd parm [1d7p]
strip :1-3,WAT
trajout part2.nc parm [1d7p]
run
clear trajin
# Combine with first and average
parm part1.parm7
trajin part1.nc parm part1.parm7
trajin part2.nc parm part1.parm7
rms first .CA
average 1iqd_1d7p_avrg.pdb .CA
On Mon, Apr 23, 2018 at 10:43 AM, Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
> 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
>>
>> _______________________________________________
>> 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
>
>
>
> --
> -------------------------
> 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
>
> _______________________________________________
> 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
--
-------------------------
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 - 08:30:03 PDT
