Re: [gmx-users] Syntax Error when Adding Ions to DNA/ligand complex
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 31 Aug 2018 at 15:01, Wahl, David M wrote: > > Hello GROMACS users, > > > I am attempting to run a molecular dynamics simulation with DNA complexed > with a small molecule. I have processed the molecule with ACPYPE, using the > GAFF, and merged the topology files into a single topology file. However, > when I attempt to use the “grompp” command before adding the ions with > genion, I get the following error: > > > Syntax error - File ligand_GMX.itp, line 3 Last line read: '[ atomtypes ]' > Invalid order for directive atomtypes > > > Originally in my single, merged topology file, I had the #include command for > the DNA chain topologies before the #include command for the ligand topology. > This is the order that resulted in the above error. > > > Whenever I moved the #include command for the ligand.itp file before the > #include command for the DNA chain .itp files, the error seemed to have gone > away. > > > Is this a valid fix for the syntax error? If it isn’t, do you have any > suggestions? If it is, why did it matter that the ligand was included before > the DNA? Under the [molecules] section I have DNA before the ligand so I’m > not understanding why it is the opposite for the #include commands? > > -- > 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.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Syntax Error when Adding Ions to DNA/ligand complex
Hello GROMACS users, I am attempting to run a molecular dynamics simulation with DNA complexed with a small molecule. I have processed the molecule with ACPYPE, using the GAFF, and merged the topology files into a single topology file. However, when I attempt to use the “grompp” command before adding the ions with genion, I get the following error: Syntax error - File ligand_GMX.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Originally in my single, merged topology file, I had the #include command for the DNA chain topologies before the #include command for the ligand topology. This is the order that resulted in the above error. Whenever I moved the #include command for the ligand.itp file before the #include command for the DNA chain .itp files, the error seemed to have gone away. Is this a valid fix for the syntax error? If it isn’t, do you have any suggestions? If it is, why did it matter that the ligand was included before the DNA? Under the [molecules] section I have DNA before the ligand so I’m not understanding why it is the opposite for the #include commands? -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Force Calculation through Pulling
Hello, I am using constant velocity method in order to pull a nanoparticle through a lipid bilayer in water solution in Gromacs. I should calculate the simultaneous force in order to take an integral over position to obtain the PMF. Do you know how can I measure the simultaneous force in order to calculate the mean force ? What command and procedure I should use? Thank you -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROMACS XRD analysis
Dear GMX users, I am trying to do x-ray diffraction analysis on my simulation results. I found in the old 4.6 version, there was an option to do this under the g_rdf module with -energy flag, but then it was removed after 5.0. The only similar module I can find now is gmx saxs module. I compared the old *g_rdf *with the new *gmx saxs* module, they seemed to give exactly the same result for my simulation. However, the result looked much like a rdf plot, as for a liquid system, I can still get signal(a peak), which doesn't seem right for an XRD plot (should be no signal for a melted system). So I am wondering if there is a tool in GMX to do an XRD analysis? Is there difference for the old g_rdf and saxs module after version 5.0? Thanks, Shi -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Documentation on gmx densorder?
Dear GMX users, I was wondering if anyone has used the gmx densorder (originally g_densorder) in the past utility in the past. I have system with an interface and the idea of " gmx densorder reduces a two-phase density distribution along an axis, computed over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a functional profile for interfacial densities" seems rather interesting. However, I haven't found any more documentation on this tool (i.e. what the binary format of its output is actually used for). If anyone has used it and has some pointers on what the output should be read with, or remembers the paper(s) it originated from it would be quite useful. Thanks, Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear gromacs user. What should be the value of spring constant (k) and rate if one wants to pull dsDNA (say bDNA of 16 bp ) surrounded by aqua (water model) during pulling using umbrella sampling . -- *With Best-Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in * *Phone n. +91 9473662491, +918777496532* -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] free energy of restraints
Dear Gromacs Users, Hi, we have added a free energy calculation of a dihedral restraint to the free energy website. Now it has exact analytical free energy calculations of all the restraints (can be used in absolute free energy calculations) and the standard bonded terms https://www.wolframcloud.com/objects/asaf.farhi/test/originalDeployment For more details: Calculation of molecular free energies in classical potentials/ A. Farhi and B. Singh, New Journal of Physics 18 023039, 2016 Thanks, Best regards, Asaf -- 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
