[gmx-users] Secondary Structure Analysis using do_dssp

Dear Gromacs Users, I am trying to analyze secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain. example (sum on whole trajectory of a chain or protein):      

[gmx-users] secondary structure analysis DSSP

Hello, I'm trying to evaluate the secondary structure of a monomer through the DSSP software. Combined with a Gromacs trajectory the output gives " Structure, Coil, B-Sheet, B-Bridge, Bend, Turn, A-Helix, 3-helix". This output is different from the standard DSSP program. I cannot find any document

Re: [gmx-users] secondary structure analysis

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. >

Re: [gmx-users] secondary structure analysis

;> >>> [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: gm

Re: [gmx-users] secondary structure analysis

10.1021/ct700324x. >> >> From: Soham Sarkar >> Sent: 24 September 2018 14:10 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] secondary structure analysis >> >> You can use do_dssp utility to generate the secondary structure >> >> On Mon, 24 Sep

Re: [gmx-users] secondary structure analysis

., 2008, > DOI:10.1021/ct700324x. > > From: Soham Sarkar > Sent: 24 September 2018 14:10 > To: gmx-us...@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 S

Re: [gmx-users] secondary structure analysis

: Soham Sarkar Sent: 24 September 2018 14:10 To: gmx-us...@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, wrote: > hi, > i am doing martini based coarsed coarse g

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, 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, seond

[gmx-users] secondary structure analysis

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 pro

[gmx-users] secondary structure analysis

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 pro

Re: [gmx-users] secondary structure analysis

You may want to familiarize yourself with how the terminal works before proceeding. You need to give the path on your machine for dssp. On Wed, May 16, 2018 at 12:13 PM, SHAHEE ISLAM wrote: > when i am using command > dssp -h > below are shown on the terminal screen > DSSP 2.0.4 options: > -h

Re: [gmx-users] secondary structure analysis

when i am using command dssp -h below are shown on the terminal screen DSSP 2.0.4 options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output --version

Re: [gmx-users] secondary structure analysis

Have you tried running the dssp command on a pdb file to ensure that it is working as intended? FYI 4.5.5 is no longer supported so you may want to consider upgrading to (the much faster) gromacs 2018. On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM wrote: > i have installed dssp2.04 in usr/local

Re: [gmx-users] secondary structure analysis

i have installed dssp2.04 in usr/local/bin. On 5/16/18, Joe Jordan wrote: > You have to point to where you have dssp installed. This may require you to > install dssp. > > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM > wrote: > >> i want calculate the secondary structure of protein in gromacs.

Re: [gmx-users] secondary structure analysis

You have to point to where you have dssp installed. This may require you to install dssp. On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM wrote: > i want calculate the secondary structure of protein in gromacs.but > when i am using this command > > do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount

[gmx-users] secondary structure analysis

i want calculate the secondary structure of protein in gromacs.but when i am using this command do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10 getting this error Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572 Fat

Re: [gmx-users] Secondary structure analysis graph rescale

Hi, http://manual.gromacs.org/online/m2p.html use gmx xpm2ps with m2p file to generate eps files. -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.g

[gmx-users] Secondary structure analysis graph rescale

Hi to whom it may concern, I would to ask something regarding gmx do_dssp analysis in Gromacs version 5.1.4. Is there any way that we can rescale the y-axis and x-axis (for major and minor ticks) of the dssp output graph in .xpm format ? and how ? your helps is highly appreciated. Thank you. -S

Re: [gmx-users] Secondary structure analysis

On 3/27/17 6:48 AM, RAHUL SURESH wrote: i found a lot libraries missing in dssp. can i obtain them using *rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/oem/Downloads/dssp* The dssp binary is all you should need. It's pre-compiled (though you can get the s

Re: [gmx-users] Secondary structure analysis

i found a lot libraries missing in dssp. can i obtain them using *rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/oem/Downloads/dssp* On Sun, Mar 26, 2017 at 9:44 PM, Souparno Adhikary wrote: > I think dssp is a useful tool for this purpose... > > Souparno > > On

Re: [gmx-users] Secondary structure analysis

I think dssp is a useful tool for this purpose... Souparno On 26 Mar 2017 19:50, "Justin Lemkul" wrote: > > > On 3/26/17 8:21 AM, RAHUL SURESH wrote: > >> I use gromacs 2016.1 version. How to do secondary structure analysis ? >> >> > http://manual.gromacs.org/documentation/2016.1/user-guide/ >

Re: [gmx-users] Secondary structure analysis

On 3/26/17 8:21 AM, RAHUL SURESH wrote: I use gromacs 2016.1 version. How to do secondary structure analysis ? http://manual.gromacs.org/documentation/2016.1/user-guide/cmdline.html#protein-specific-analysis -Justin -- == Justin A. Lemkul, P

[gmx-users] Secondary structure analysis

I use gromacs 2016.1 version. How to do secondary structure analysis ? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!