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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Received on Tue Dec 11 2012 - 07:30:02 PST
