Hi Dan,
Thanks for looking into this.
It turns out that when I use a prmtop file as 'parm', instead of a pdb
file, then it works fine for me too.
Is that what you tested?
It was just when I used a pdb as 'parm' that I got the problems.
[for those searching the archives:] The problems I had with the mask
were due to me using parenthesis instead of single quotes. So, this is
wrong:
atomicfluct out test.dat (:74 & !.N,H,CA,HA,C,O) bymask
It should be:
atomicfluct out test.dat ':74 & !.N,H,CA,HA,C,O' bymask
I'm happy to just create 'stripped' prmtops and use those for my analysis.
Let me know if you still would like the pdb files of my system to test with.
Thanks,
Marc
On 12 December 2012 18:38, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I'm not able to reproduce your error with a simple test system in
> ptraj or cpptraj. Something like:
>
> atomicfluct out fluct.6.dat :6 byres
>
> works fine for me:
>
> 6 2.988928
>
> So maybe it's something particular to your system. Could you send me
> off-list the PDB files with which you are getting this behavior?
> Thanks.
>
> -Dan
>
> On Tue, Dec 11, 2012 at 8:00 AM, Marc van der Kamp
> <marcvanderkamp.gmail.com> wrote:
>> Dear all,
>>
>> I would like to calculate the (mass-weighted) RMSF (positional
>> fluctuations) for a specific residue side chain.
>> This seems a simple task, but I can't seem to get ptraj or cpptraj to
>> get me to do it.
>>
>> To test, I've used a simple input file (reading just three snapshots,
>> as separate pdb files).
>> For ptraj, I used the following:
>>
>> avg50-250.pdb
>> reference avg50-250.pdb
>> trajin avg50.pdb
>> trajin avg50-250.pdb
>> trajin avg500-250.pdb
>>
>> When I follow this with:
>> rms reference .CA
>> atomicfluct out rmsf_ca_all.dat .CA byatom
>>
>> I get the RMSF for all CA atoms, as I expected.
>>
>> When I follow this with:
>> rms reference :72-76.CA,N,C
>> atomicfluct out rmsf_k142_1.dat :74 byres
>>
>> the rmsf_k142_1.dat file is created, but empty!
>> same for "atomicfluct out rmsf_k142_1.dat :72-76 byres" and
>> "atomicfluct out rmsf_k142_1.dat :74.CB,CG,CE,NZ bymask".
>>
>> When I use what I I'd really like to select the side-chain atoms (more
>> generic), i.e.
>> atomicfluct out rmsf_k142_1.dat ( :74 & !.N,H,CA,HA,C,O ) bymask
>> ptraj stops with "ERROR in parsing atom mask: unbalanced parentheses
>> in expression".
>>
>> Only in 'byatom' mode output IS generated, e.g. "atomicfluct out
>> rmsf_k142_1.dat :74 byatom", but this generates (as it should do)
>> atom-specific fluctuations. I could of course calculate the
>> mass-weighted average fluctuations from that, but I'd rather do this
>> with ptraj/cpptraj...
>>
>> I have also tried the above with cpptraj, with the necessary
>> adjustments to the rms(d) commands (and "parm avg50-250.pdb" for the
>> initial prmtop reading).
>> Again, RMSF for all CA atoms is calculated just fine, and for just
>> atoms in one residue using 'byatom' is fine too.
>> cpptraj doesn't have a problem with the combined mask ( :74 &
>> !.N,H,CA,HA,C,O ) like ptraj had.
>> However, when I try 'byres' or 'bymask' instead of 'byatom', I get:
>> ACTION OUTPUT:
>> PTRAJ ATOMICFLUCT: Dumping atomic positional fluctuations
>> Segmentation fault
>>
>> It would be great if someone could shine a light on this...
>>
>> Thanks!
>> Marc
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
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Received on Thu Dec 13 2012 - 02:30:02 PST
