hi,
my self compiled ptraj seems to be unable to find the secondary structure
(CentOS-5.5 x86_64 gcc/gcc44/intel-10.1.025 or intel-11.1.072).
testcase attached:
1) GSCASVCGV.pdb is a "canonical" alpha helix created from the sequence listed
at the modeller wiki at
http://www.salilab.org/modeller/wiki/Make%20alpha%20helix and vmd script at
http://mem.bio.pitt.edu/?q=node/62
the pdb file is attached to this mail, it was built with the following script
<cut build_helix.vmd>
#!/usr/bin/tclsh
set amseq [lindex $argv 0]
mol new atoms 1
package require molefacture
::Molefacture::set_phipsi -57 -47
::Molefacture::build_textseq $amseq
set allSel [atomselect top "resid < 9999"]
$allSel writepdb $amseq.pdb
</cut>
vmd < build_helix.vmd -args GSCASVCGV
2) stride (from vmd 1.8.7
http://www.ks.uiuc.edu/Research/vmd/) and dssp
(dsspcmbi version from
http://binf.gmu.edu/software/DSSPCMBI.html)
were used to calculate the helix properties of the peptide
dssp GSCASVCGV.pdb > GSCASVCGV.dssp
stride GSCASVCGV.pdb > GSCASVCGV.stride
both programs agree: it's an helix
both outputs are also attached
3) run ptraj to identify the secondary structure of GSCASVCGV.pdb
<cut GSCASVCGV.in>
trajin GSCASVCGV.pdb
secstruct
</cut>
ptraj GSCASVCGV.pdb < GSCASVCGV.in
all my ptraj version report no helicoidal content :(
(AmberTools-1.4 with bugfix 1-13 and 1-16)
Best regards,
Tru
--
Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru.pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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Received on Fri Mar 11 2011 - 17:00:04 PST
