DOCK 6 FAQDOCK 6 FAQ Copyright 2. Regents of the University of California. All Rights Reserved Last updated. April 2. 6, 2. 01. General Questions. What is the current release of DOCK The current release is version 6. April 2. 01. 7. Should I upgrade to the current release In general, yes. In particular, bug fixes and basic improvements will make the upgrade. Where do I get the dms program, and how much does it cost UCSF Chimeras Tool. Chimera versions 1. The dms program is distributed by the Computer Graphics Lab at UCSF. It is free of charge. To download a copy of dms, go to this link. What if I have a question that. You can join the. General Questions. What is the current release of DOCK The current release is version 6. April 2017. A fast and easy sourcelevel XML and Json Editor, XML Marker uses a combination of syntaxhighlighting editor, tree view, and table views to help you get a better. DOCK. the archives before asking your question. Installation Questions. How is dms installed UCSF Chimeras Tool. Chimera versions 1. The dms program. description at the UCSF Computer Graphics Lab. README file in the dms distribution provide details. Here is a quick start example. Edit GNUmakefile per the README change LIBDIR and BINDIR. Some reported problems are caused by invalid. LIBDIR and BINDIR definitions. Ensure that these directories actually exist create them. DOCK Fans mail archives before posting dms related questions. Should AMBERHOME be set No. Xex Menu Live more. In fact, for DOCK versions through. AMBERHOME environment variable will cause. DOCK Amber score preparation procedure. Delete-All-Files-in-Directory-Except-One-Few-with-Extensions.png' alt='Dos2unix Multiple Files Handbrake' title='Dos2unix Multiple Files Handbrake' />Dos2unix Multiple Files To One PdfDos2unix Multiple Files PdfFor examples on undefining AMBERHOME see the. FAQ. When I test or run DOCK with the amberscore. I get Error from amberizeligand. Entering directory dock. Coordinate and parameter files for the Receptor 1. The AMBER score tagged mol. Splitting the multiple Ligand mol. The single mol. 2 files will have the prefix lig. The number of single Ligand mol. Generating coordinate and parameter files for Ligands and Complexes. Generating AM1 BCC charges. This may be time consuming. Ligand lig. 1 has total charge 0. Error from amberizeligand the name of the ligand is. Examine amberizeligand. What is causing the error and how do I fix itIt is very likely that the AMBERHOME environment variable. DOCK antechamber. Try undefining AMBERHOME. AMBERHOME for the bash and similar shells. AMBERHOME for the tcsh and similar shells. If this does not fix the problem then read the rest of this FAQ. Known causes are. AMBERHOME environment variable. AMBERHOME environment variable that. AMBER installation. AMBERHOME environment variable that. AMBER9 through AMBER1. Amber. Tools installation. The problem is usually that antechamber uses AMBERHOME. This can cause antechamber to fail. Thus, the amberizeligand step of the DOCK amber preparation scripts. Century Gothic Bold Otf Download. The error is inside the. The simplest patch is to undefine AMBERHOME. DOCK supplied. AMBER programs. A possible cause is a faulty DOCK installation. When I build DOCK. I get a yacc Command not found error yacc parser. Command not found. Error 1. 27. What is causing the error and how do I fix it The tleap program. Unix command names are yacc and bison. All classical Unices have yacc. Linuces usually have yacc. But this command not found error is caused by a missing parser generator. It may be that some users are not installing enough of their Linux. Here are some suggestions. Verify that yacc missing. Look for a parser generator on your machine. Likely candidates are bison. If it is found then. YACC definition. that is equal to bison, i. YACCbison y. Restart the installation cd install make install Install a parser generator if one is not found. The appropriate Linux package is usually named byacc. The installation command. Bison GNU parser generator. When I compile DOCK. I get an mmolex Undefined symbols error g O2 o dock. Undefined symbols mmolexmake dock. Error 1. What is causing the error and how do I fix itDOCK 6 requires a lexical analyzer generator. Unix command names are lex and flex. All classical Unices have lex. Linuces usually have flex. But this undefined symbol is caused by a missing lexical analyzer generator. It may be that some users are not installing enough of their Linux. In particular, dock. Here are some suggestions. Verify that dock. Look for a lexical analyzer generator on your machine. Verify the definition of the macro LEX in the configuration. LEX should be. assigned the name of your lexical analyzer generator. Install a lexical analyzer generator if one is not found. The Fast Lexical Analyzer. In DOCK 6. 1 and later. Change directory to dock. Copy that file to dock. This file was generated by flex version 2. Red Hat Enterprise Linux AS release 3 Taroon Update 6. Edit dock. 6installconfig. LEX definition. equal to flex, i. LEX flex. Restart the installation cd install make install In DOCK 6. Change directory to dock. Download lex. mmoptions. This file was generated by flex version 2. Red Hat Enterprise Linux AS release 3 Taroon Update 6. Copy it to dock. 6srcdocknablex. Edit dock. 6installconfig. LEX definition. equal to flex, i. LEX flex. Restart the installation cd install make install. Old Installation Questions. When I test or run DOCK with the amberscore. I get a getpdb cant open file lig. Reading parm file 1lgu. Error 1. What is causing the error and how do I fix it Known causes are. AMBERHOME environment variable. AMBERHOME environment variable that. AMBER installation. AMBERHOME environment variable that. AMBER9 installation. The problem is usually that antechamber uses AMBERHOME to determine. This can cause antechamber to fail. Thus, one of the steps of the DOCK amber preparation scripts. The error is buried inside one of the. The simplest patch is to undefine AMBERHOME. DOCK supplied. AMBER programs. A possible cause is a faulty DOCK installation. When I compile DOCK with Intel compilers. I get a multiple definition of main error ifort O2 grid. In function main. In function main. MAIN. make2 grid Error 1. What is causing the error and how do I fix itWhen mixing C and Fortran some compilers. C main function. Some do not, such as Intel compilers, and that results in link errors. The solution for Intel compilers is to include. The can be done via DOCKBUILDFLAGS or by modifying. Makefile. In release 6. LINKWITHOUTFORTRANMAIN, to implement a simple. When I compile DOCK. I get syntax error before numeric constant g c DBUILDDOCKWITHMPI DMPICHIGNORECXXSEEK Iinclude O2 o ambertyper. In file included from usrincludempi. What is causing the error and how do I fix it This error is due to an incompatibility. MPICH2 installation and the. DOCK 6. Because DOCK 6 does not use the MPI C bindings, this issue can be. MPICHSKIPMPICXX. This can be done on the command line via. DOCKBUILDFLAGS DMPICHSKIPMPICXX. DOCK 6 configuration file config. Phtls 7 Edicao Em Pdf. CFLAGS, e. g. CFLAGS DBUILDDOCKWITHMPI DMPICHIGNORECXXSEEK DMPICHSKIPMPICXX IMPICHHOMEinclude O2. In release 6. 1 we modified the DOCK 6 configuration files as above. See MPI C Bindings for background information. Note that DOCK 6 does use some MPI C bindings and does not use any MPI. Fortran bindings. Platform Specific Questions. What is the impact of Windows and DOS line terminators Disk Operating System DOS which underlies Windows. One can translate the DOS line terminators to UNIX. Cygwins cygutils package or using a web service. Alternatively, some editors can change line terminators. For example, to change the line terminators in the rec. Note that the Write DMS tools in pre June 3, 2. Chimera versions. DOS line terminators. Use a later Chimera version or translate. What are the prerequisites for installing on Mac OS X Versions 6 of DOCK officially support.