From gyorgy.abrusan at gmail.com Fri Feb 8 13:19:51 2019 From: gyorgy.abrusan at gmail.com (Gyorgy Abrusan) Date: Fri, 8 Feb 2019 21:19:51 +0000 Subject: [Dock-fans] sphgen issues Message-ID: Hi guys, I have encountered issues with sphgen, it crashes on some of my (relatively large 1100 residues) receptor files. I wonder whether there is an alternative tool I could use, or a different set of parameters that will work well for large receptors. Best wishes, Gyorgy Abrusan PS: I am using the default parameters in in INSPH: receptor_noH.ms R X 0.0 4.0 1.4 receptor_noH.sph -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20190208/7f771a3c/attachment.html From brianfochtman at gmail.com Fri Feb 8 20:05:04 2019 From: brianfochtman at gmail.com (Brian Fochtman) Date: Fri, 8 Feb 2019 23:05:04 -0500 Subject: [Dock-fans] sphgen issues In-Reply-To: References: Message-ID: Hi Gyorgy, Sphgen.cpp is a rewrite of sphgen which works better for large receptors. The input and output is the same so your current script will work. http://dock.compbio.ucsf.edu/Contributed_Code/sphgen_cpp.htm Best, Brian On Fri, Feb 8, 2019 at 4:15 PM Gyorgy Abrusan wrote: > > Hi guys, > > I have encountered issues with sphgen, it crashes on some of my > (relatively large 1100 residues) receptor files. I wonder whether there is > an alternative tool I could use, or a different set of parameters that will > work well for large receptors. > > Best wishes, > Gyorgy Abrusan > > PS: I am using the default parameters in in INSPH: > receptor_noH.ms > R > X > 0.0 > 4.0 > 1.4 > receptor_noH.sph > > > > > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://mailman.docking.org/mailman/listinfo/dock-fans > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20190208/b6ff91ea/attachment.html From golani at uwm.edu Mon Feb 18 12:01:02 2019 From: golani at uwm.edu (Lalit K Golani) Date: Mon, 18 Feb 2019 20:01:02 +0000 Subject: [Dock-fans] HELP; Installation of DOCK6 on window 10 with Cygwin Message-ID: Hi, I am trying to install and run DOCK6 on window 10 with Cygwin. Steps I did after I downloaded dock6 1. Downloaded Cygwin with devel 2. tar -zxvf dock.6.9.tar.gz 3. cd dock6/install 4. ./configure gnu 5. make all 6. cd test 7. make test then after all these I tried to run the program and I search dock6.exe file was in dock6/bin folder, I executed it as ./dock6.exe, the Cygwin terminal give me this -------------------------------------- DOCK v6.9 Released November 2018 Copyright UCSF -------------------------------------- Usage: dock6 -i filename.in [-o filename.out] [-v] Please help me, how can I open the software I thought I will be opening an interactive window like chimera or pymol. I am doing anything wrong? I do not have any experience with Linux. Thanks Regards Lalit K Golani, Ph.D Post-Doctoral Research Associate, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20190218/c664b19c/attachment.html From tbalius at aol.com Tue Feb 19 10:59:52 2019 From: tbalius at aol.com (Trent E. Balius) Date: Tue, 19 Feb 2019 18:59:52 +0000 (UTC) Subject: [Dock-fans] HELP; Installation of DOCK6 on window 10 with Cygwin References: <1318000481.1705452.1550602792398.ref@mail.yahoo.com> Message-ID: <1318000481.1705452.1550602792398@mail.yahoo.com> Hi Lalit, There is no graphical user interface in DOCK.? You must run it on the command line.? Here are some good tutorials for how to run DOCK6: http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials http://ringo.ams.sunysb.edu/index.php/2018_DOCK_tutorial_1_with_PDBID_2NNQ http://ringo.ams.sunysb.edu/index.php/2018_DOCK_tutorial_2_with_PDBID_1C87 you can also use the DOCK manual as a reference: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm I hope that this helps, Trent ====================================== Trent E. Balius, PhD URL: http://docking.org/~tbalius ====================================== -----Original Message----- From: Lalit K Golani To: dock-fans at docking.org Sent: Mon, Feb 18, 2019 12:01 pm Subject: [Dock-fans] HELP; Installation of DOCK6 on window 10 with Cygwin #yiv9116939945 #yiv9116939945 #yiv9116939945 -- filtered {panose-1:2 4 5 3 5 4 6 3 2 4;}#yiv9116939945 filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv9116939945 filtered {panose-1:2 11 6 9 4 5 4 2 2 4;}#yiv9116939945 p.yiv9116939945MsoNormal, #yiv9116939945 li.yiv9116939945MsoNormal, #yiv9116939945 div.yiv9116939945MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9116939945 a:link, #yiv9116939945 span.yiv9116939945MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv9116939945 a:visited, #yiv9116939945 span.yiv9116939945MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv9116939945 p.yiv9116939945MsoListParagraph, #yiv9116939945 li.yiv9116939945MsoListParagraph, #yiv9116939945 div.yiv9116939945MsoListParagraph {margin-top:0in;margin-right:0in;margin-bottom:0in;margin-left:.5in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9116939945 span.yiv9116939945EmailStyle17 {font-family:sans-serif;color:windowtext;}#yiv9116939945 .yiv9116939945MsoChpDefault {font-family:sans-serif;}#yiv9116939945 filtered {margin:1.0in 1.0in 1.0in 1.0in;}#yiv9116939945 div.yiv9116939945WordSection1 {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 filtered {}#yiv9116939945 ol {margin-bottom:0in;}#yiv9116939945 ul {margin-bottom:0in;}#yiv9116939945 #yiv9116939945 Hi, ? I am trying to install and run DOCK6 on window 10 with Cygwin. Steps I did after I downloaded dock6 1.??????Downloaded Cygwin with devel 2.??????tar -zxvf dock.6.9.tar.gz 3.??????cd dock6/install 4.??????./configure gnu 5.??????make all 6.??????cd test 7.??????make test ? then after all these I tried to run the program and I search dock6.exe file was in dock6/bin folder, I executed it as ./dock6.exe, the Cygwin terminal give me this ? ? -------------------------------------- DOCK v6.9 ? Released November 2018 Copyright UCSF -------------------------------------- ? ? Usage: ??????? dock6 -i filename.in [-o filename.out] [-v] ? Please help me, how can I open the software I thought I will be opening an interactive window like chimera or pymol. I am doing anything wrong? I do not have any experience with Linux. ? Thanks Regards ? Lalit K Golani, Ph.D Post-Doctoral Research?Associate, ? _______________________________________________ Dock-fans mailing list Dock-fans at docking.org http://mailman.docking.org/mailman/listinfo/dock-fans -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20190219/23ca91c5/attachment.html