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
>
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--
-------------------------
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 Wed Dec 12 2012 - 11:00:02 PST
