[AMBER] AmberTools 1.4 possible bug for secstruct (test case attached)

From: Tru Huynh <tru.pasteur.fr>
Date: Sat, 12 Mar 2011 01:30:57 +0100


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

the pdb file is attached to this mail, it was built with the following script

<cut build_helix.vmd>

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

        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
        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,

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
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