[gmx-users] DSSP output
Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? And how to plot the data of the -sc output from do_dssp? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP output
On 11/7/13 8:24 AM, Anirban wrote: Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? The output of scount.xvg has the percentages, but it's also trivial to do it for one snapshot. The contents of scount.xvg are the number of residues present in each type of secondary structure, and you know the total number of residues... And how to plot the data of the -sc output from do_dssp? Like any multiple data set. xmgrace -nxy -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dssp output of CG structure of 1K4C
Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dssp output of CG structure of 1K4C
sunny mishra wrote: Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Not likely. DSSP calculates secondary structure from hydrogen bonds, which will be absent in a CG model. The script you refer to (dssp2ssd.py) does not use DSSP to calculate secondary structure; it simply converts DSSP output to the .ssd file needed by MARTINI. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dssp output of CG structure of 1K4C
Hi Justin, Thanks for the expedient reply. So in that case I cannot get the dssp output of my CG structure for sure. So in that case do I have to get the .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file of 1K4c_clean.pdb in order to proceed. Am I right? Sunny On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: sunny mishra wrote: Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Not likely. DSSP calculates secondary structure from hydrogen bonds, which will be absent in a CG model. The script you refer to (dssp2ssd.py) does not use DSSP to calculate secondary structure; it simply converts DSSP output to the .ssd file needed by MARTINI. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dssp output of CG structure of 1K4C
sunny mishra wrote: Hi Justin, Thanks for the expedient reply. So in that case I cannot get the dssp output of my CG structure for sure. So in that case do I have to get the .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file of 1K4c_clean.pdb in order to proceed. Am I right? Right, to generate the MARTINI topology you need both .ssd and .seq files. -Justin Sunny On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sunny mishra wrote: Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Not likely. DSSP calculates secondary structure from hydrogen bonds, which will be absent in a CG model. The script you refer to (dssp2ssd.py) does not use DSSP to calculate secondary structure; it simply converts DSSP output to the .ssd file needed by MARTINI. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dssp output of CG structure of 1K4C
OK. Thanks a lot justin On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: sunny mishra wrote: Hi Justin, Thanks for the expedient reply. So in that case I cannot get the dssp output of my CG structure for sure. So in that case do I have to get the .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file of 1K4c_clean.pdb in order to proceed. Am I right? Right, to generate the MARTINI topology you need both .ssd and .seq files. -Justin Sunny On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: sunny mishra wrote: Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Not likely. DSSP calculates secondary structure from hydrogen bonds, which will be absent in a CG model. The script you refer to (dssp2ssd.py) does not use DSSP to calculate secondary structure; it simply converts DSSP output to the .ssd file needed by MARTINI. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
