Re: [gmx-users] DSSP problem
On 10/13/13 11:56 PM, Mass wrote: Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr Try giving readable permissions to all, i.e. chmod +r. With I/O errors, the answer is always one of: (1) file does not exist, (2) file has wrong permissions, or (3) cannot write to disk for space or permission reasons. -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
Re: [gmx-users] DSSP problem
Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l total 92332632 -rw-rw-r-- 1 Mass Mass 0 Sep 8 19:46 310Helix.dat -rw--- 1 Mass Mass 371878 Aug 21 07:39 3BLG_115XrayWater.top -rw-rw-r-- 1 Mass Mass 282249 Sep 8 19:46 aHelix.dat -rw-rw-r-- 1 Mass Mass 12963 Sep 9 20:00 average.pdb -rw-rw-r-- 1 Mass Mass 12962 Aug 22 21:49 #average.pdb.1# -rw-rw-r-- 1 Mass Mass 12963 Sep 1 20:18 #average.pdb.2# -rw-rw-r-- 1 Mass Mass 39371 Aug 23 10:50 bLac_orig_md2-3_atomic-sas.xvg -rw-rw-r-- 1 Mass Mass 1180585 Aug 22 22:20 bLac_orig_md2-3_radius-of-gyration.xvg -rw-rw-r-- 1 Mass Mass6151 Aug 23 10:50 bLac_orig_md2-3_residue-sas.xvg -rw-rw-r-- 1 Mass Mass 538412 Aug 22 20:15 bLac_orig_md2-3_rmsd-Calpha-vs-start.xvg -rw-rw-r-- 1 Mass Mass2791 Aug 22 21:49 bLac_orig_md2-3_rmsf-per-residue.xvg -rw-rw-r-- 1 Mass Mass 6739262 Aug 23 13:33 bLac_orig_md2-3_SecStruc.dat -rw-rw-r-- 1 Mass Mass 1180736 Aug 23 10:50 bLac_orig_md2-3_solvent-accessible-surface.xvg -rw-rw-r-- 1 Mass Mass 815104 Aug 23 10:32 #bLac_orig_md2-3_solvent-accessible-surface.xvg.1# -rw-rw-r-- 1 Mass Mass 4696839648 Aug 22 15:58 bLac_orig_md2-3.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:31 bLac_orig_md2.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:31 bLac_orig_md2.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:31 bLac_orig_md2.gro -rw--- 1 Mass Mass 7213156 Aug 21 07:39 bLac_orig_md2.log -rw--- 1 Mass Mass 1539720 Aug 21 06:31 bLac_orig_md2_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 07:39 bLac_orig_md2.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr -rw--- 1 Mass Mass 2348494832 Aug 21 06:41 bLac_orig_md2.xtc -rw-rw-r-- 1 Mass Mass 7045242668 Sep 1 18:41 bLac_orig_md3-4.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md3.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:19 bLac_orig_md3.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:19 bLac_orig_md3.gro -rw--- 1 Mass Mass 7212876 Aug 21 06:31 bLac_orig_md3.log -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md3_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 06:31 bLac_orig_md3.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 07:39 bLac_orig_md3.trr -rw--- 1 Mass Mass 2348579612 Aug 21 06:31 bLac_orig_md3.xtc -rw-rw-r-- 1 Mass Mass 39519 Sep 9 20:54 bLac_orig_md4-5_atomic-sas.xvg -rw-rw-r-- 1 Mass Mass 39542 Sep 1 21:56 #bLac_orig_md4-5_atomic-sas.xvg.1# -rw-rw-r-- 1 Mass Mass 2360604 Sep 9 20:11 bLac_orig_md4-5_radius-of-gyration.xvg -rw-rw-r-- 1 Mass Mass 2360602 Sep 1 21:02 #bLac_orig_md4-5_radius-of-gyration.xvg.1# -rw-rw-r-- 1 Mass Mass6135 Sep 9 20:54 bLac_orig_md4-5_residue-sas.xvg -rw-rw-r-- 1 Mass Mass6158 Sep 1 21:56 #bLac_orig_md4-5_residue-sas.xvg.1# -rw-rw-r-- 1 Mass Mass 1098421 Sep 9 19:50 bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg -rw-rw-r-- 1 Mass Mass 1098406 Sep 1 19:37 #bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg.1# -rw-rw-r-- 1 Mass Mass2815 Sep 9 20:00 bLac_orig_md4-5_rmsf-per-residue.xvg -rw-rw-r-- 1 Mass Mass2799 Sep 1 20:18 #bLac_orig_md4-5_rmsf-per-residue.xvg.1# -rw-rw-r-- 1 Mass Mass 6739262 Sep 8 19:45 bLac_orig_md4-5_SecStruct.dat -rw-rw-r-- 1 Mass Mass 2360697 Sep 9 20:54 bLac_orig_md4-5_solvent-accessible-surface.xvg -rw-rw-r-- 1 Mass Mass 2360696 Sep 1 21:56 #bLac_orig_md4-5_solvent-accessible-surface.xvg.1# -rw-rw-r-- 1 Mass Mass 9393557496 Sep 1 18:53 bLac_orig_md4-5.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md4.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:08 bLac_orig_md4.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:08 bLac_orig_md4.gro -rw--- 1 Mass Mass 7212890 Aug 21 06:08 bLac_orig_md4.log -rw--- 1 Mass Mass 1539720 Aug 21 04:58 bLac_orig_md4_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 06:08 bLac_orig_md4.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 06:19 bLac_orig_md4.trr -rw--- 1 Mass Mass 2348637800 Aug 21 05:08 bLac_orig_md4.xtc -rw--- 1 Mass Mass 1539720 Aug 21 04:58 bLac_orig_md5.cpt -rw--- 1 Mass Mass 7561608 Aug 21 04:58 bLac_orig_md5.edr -rw--- 1 Mass Mass 4412810 Aug 21 04:58 bLac_orig_md5.gro -rw--- 1 Mass Mass 7212675 Aug 21 04:58 bLac_orig_md5.log -rw--- 1 Mass Mass 1539720 Aug 21 06:08 bLac_orig_md5_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 04:58 bLac_orig_md5.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 06:08 bLac_orig_md5.trr -rw--- 1 Mass Mass 2348549636 Aug 21 06:19 bLac_orig_md5.xtc -rw--- 1 Mass Mass 10315 Aug 21 07:39 bLac_orig.p1n14-c.69215.err -rw--- 1 Mass Mass 0 Aug 21 07:39 bLac_orig.p1n14-c.69215.out -rw--- 1 Mass Mass 10312 Aug 21 06:31
[gmx-users] DSSP problem
Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? -- 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 problem
On 10/12/13 6:08 PM, Mass wrote: Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? Please provide the copied and pasted output of ls -l in that directory. -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
Re: [gmx-users] dssp problem
On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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 problem
http://biskit.pasteur.fr/install/applications/dssp wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip unzip dsspcmbi.zip cd dssp ./DsspCompileGCC cd .. sudo mv dssp /usr/local/src/ cd /usr/local/bin sudo ln -s ../src/dssp/dsspcmbi . lina On Sat, Dec 25, 2010 at 8:45 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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 problem
Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Best wishes -- 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 problem
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel mfbil...@gmail.com wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. You should issue: export DSSP=/home/m/DSSP See, /home/m/DSSP is actually the /path/to/dssp in your case. Terry And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Best wishes -- 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 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 problem
pawan raghav wrote: I have download dsspcmbi.zip and extract the dssp folder into /cygdrive/c/cygwin/usr/local/bin/ directory. Then set the environment variable export DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to my folder by using cd where all my md files were present i.e. /cygdrive/c/gromacs-4.0.7. At last I executed the command do_dssp -f traj.xtc -s md.tpr -n index.ndx -aa area.xvg after preformed this I still got an error i.e. Fatal error: failed to execute command: /cygdrive/c/cygwin/usr/local/bin/dssp ddrN1s8q dd4bcjqa /dev/null 2 /dev/null Please rectify this.. Your environment variable is wrong. If you placed a dssp folder in /usr/local/bin, then the actual executable is located in /usr/local/bin/dssp/dssp. Have a look at the usage notes: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin -- Pawan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] DSSP problem
Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error Permission Denied even i m super user for the machine (root). [r...@localhost ~]# dssp bash: /usr/local/bin/dssp: Permission denied [r...@localhost ~]# Plaese any body tell the solution for this problem... Regard Rituraj -- The future belongs to those who believe in the beauty of their dreams. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 problem
rituraj purohit wrote: Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error Permission Denied even i m super user for the machine (root). [r...@localhost ~]# dssp bash: /usr/local/bin/dssp: Permission denied [r...@localhost ~]# Plaese any body tell the solution for this problem... You may still need execute permissions on the original executable. You should not ever be running as root when not installing software or maintaining the system. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] DSSP problem
: 3 Date: Thu, 04 Jun 2009 01:24:32 -0500 From: Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx Subject: [gmx-users] Replacing the PRODRG charges To: gmx-users@gromacs.org Message-ID: 1244096672.4a2768a0e4...@webmail.ibt.unam.mx Content-Type: text/plain; charset=ISO-8859-1 I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and OPLS forcefields)?. Or will it be mixing forcefields?. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- Message: 4 Date: Thu, 04 Jun 2009 16:29:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Replacing the PRODRG charges To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a2769af.6000...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Lucio Ricardo Montero Valenzuela wrote: I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and OPLS forcefields)?. Or will it be mixing forcefields?. That depends on your target forcefield for your MD. Mark -- Message: 5 Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST) From: amri ta amrita0092...@yahoo.co.in Subject: [gmx-users] how to include ionic strength To: gmx-users@gromacs.org Message-ID: 418624.33836...@web8708.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. Thanks in advance. Amrita Paul Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090604/84086c55/attachment-0001.html -- Message: 6 Date: Thu, 04 Jun 2009 17:09:35 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to include ionic strength To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a27732f.1020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed amri ta wrote: Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. If you do some tutorial material, you will find out the procedure for adding ions. Finding out how many ions to add is for you to calculate :-) Mark -- Message: 7 Date: Thu, 4 Jun 2009 12:52:32 +0530 From: rituraj purohit riturajpuro...@gmail.com Subject: [gmx-users] DSSP problem To: gmx-users@gromacs.org Message-ID: 685cca3f0906040022j73103651p972ec3922736e...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error Permission Denied even i m super user for the machine (root). [r...@localhost ~]# dssp bash: /usr/local/bin/dssp: Permission denied [r...@localhost ~]# Plaese any body tell the solution for this problem... Regard Rituraj -- The future belongs to those who believe in the beauty of their dreams. -- Message: 8 Date: Thu, 04 Jun 2009 17:28:13 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] DSSP problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a27778d.1060...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed rituraj purohit wrote: Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy
Re: [gmx-users] DSSP problem
how to do this kind of calculation or any published papers doing this things? anyhelp is greatly appreciate! Best Wishes R-X Gu -- Message: 3 Date: Thu, 04 Jun 2009 01:24:32 -0500 From: Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx Subject: [gmx-users] Replacing the PRODRG charges To: gmx-users@gromacs.org Message-ID: 1244096672.4a2768a0e4...@webmail.ibt.unam.mx Content-Type: text/plain; charset=ISO-8859-1 I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and OPLS forcefields)?. Or will it be mixing forcefields?. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- Message: 4 Date: Thu, 04 Jun 2009 16:29:03 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Replacing the PRODRG charges To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a2769af.6000...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Lucio Ricardo Montero Valenzuela wrote: I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and OPLS forcefields)?. Or will it be mixing forcefields?. That depends on your target forcefield for your MD. Mark -- Message: 5 Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST) From: amri ta amrita0092...@yahoo.co.in Subject: [gmx-users] how to include ionic strength To: gmx-users@gromacs.org Message-ID: 418624.33836...@web8708.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. Thanks in advance. Amrita Paul Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090604/84086c55/attachment-0001.html -- Message: 6 Date: Thu, 04 Jun 2009 17:09:35 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to include ionic strength To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a27732f.1020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed amri ta wrote: Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. If you do some tutorial material, you will find out the procedure for adding ions. Finding out how many ions to add is for you to calculate :-) Mark -- Message: 7 Date: Thu, 4 Jun 2009 12:52:32 +0530 From: rituraj purohit riturajpuro...@gmail.com Subject: [gmx-users] DSSP problem To: gmx-users@gromacs.org Message-ID: 685cca3f0906040022j73103651p972ec3922736e...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error Permission Denied even i m super user for the machine (root). [r...@localhost ~]# dssp bash: /usr/local/bin/dssp: Permission denied [r...@localhost ~]# Plaese any body tell the solution for this problem... Regard Rituraj -- The future belongs to those who believe in the beauty of their dreams. -- Message: 8 Date: Thu, 04 Jun 2009 17:28:13 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject
Re: [gmx-users] DSSP problem
rituraj purohit wrote: Dear mark Where i can get the file with permission. I downloaded from http://swift.cmbi.kun.nl/gv/dssp/ Please do not send copies of entire digests in your emails. That breaks searches and wastes time and bandwidth. You give the file permissions in the standard Unix way with chmod. Please try to search for your own solutions first - 5 seconds with Google should result in this page: http://en.wikipedia.org/wiki/File_system_permissions Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
