[gmx-users] secondary structure analysis

[SHAHEE ISLAM]

by using only the .gro is it possible to calculate the secondary
structure of protein.because when i am using this comment
do_dssp -s aa_charmm-eq.gro -n ../index-p.ndx -sss scount-p-0-1.xvg -o
ss-p-0-1.xpm
the error is
Can not open file:
traj.xtc
because i have the all atom gro file (obtained by converting cg.gro to
all atom gro file.) i cant use the .xtc file ,because it is a martini
cg.xtc file.
thanking you
shahee

On 9/24/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> thank you so much for your quick reply.if i convert the coarse grained
> pdb into all atom gro file,then vmd can calculate the secondary
> structure.is this correct or there are other way to calculate the
> change of secondary structure of protein.
>
> On 9/24/18, P C Kroon <p.c.kroon at rug.nl> wrote:
>> Hi Soham,
>>
>> In normal Martini you *can NOT* see secondary structure changes. It is
>> usually fixed using either elastic bonds or extended dihedrals. If you
>> apply
>> neither it will generally collapse into a spherical ball of entropy.
>> Please
>> refer to e.g. Monticelli et al. [1]
>> Also, in general, analysis tool (VMD, DSSP) don’t like CG structures.
>> They
>> don’t recognise the names of the particles (and to be honest, I don’t
>> blame
>> them)
>>
>> Peter
>>
>> [1] L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P.
>> Tieleman, S. J. Marrink, J. Chem. Theory Comput., 2008,
>> DOI:10.1021/ct700324x.
>>
>> From: Soham Sarkar
>> Sent: 24 September 2018 14:10
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] secondary structure analysis
>>
>> You can use do_dssp utility to generate the secondary structure
>>
>> On Mon, 24 Sep 2018, 5:34 pm SHAHEE ISLAM, <islamshahee at gmail.com> wrote:
>>
>>> hi,
>>> i am doing martini based coarsed coarse grained simulation in
>>> gromacs.after getting the coarse grained structure ,i can convert cg
>>> pdb it to the gro file.using vmd, seondary structure can be
>>> analysed.can any one suggest what may be the best way to calculate the
>>> secondary structure change of protein.
>>> thanking you
>>> shahee
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>