[gmx-users] Assigning protonation states using Amber ff
Dear gromacs users, I am carrying out solvent-free simulations of a DNA-protein complex using the Amber forcefield. Amber automatically assigns negative charges to the DNA. Is there any way to have neutral DNA? Similarly, I would like to select which Arg residues are protonated, however the Amber forcefield does not appear to support deprotonated Arg. Is there any way around this? Previously I have been able to assign the protonation state of all basic and acidic residues with the OPLS forcefield (using the interactive commands in pdb2gmx), however with DNA included, I figured I needed to use Amber. Any advice on this would be appreciated! Thanks in advance, Zoe Hall Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- 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] Adding OPLS-UA forcefield
Dear users, How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 4.5.3? Thanks in advance, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- 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] Re: Simluations in vacuum - energy increase
Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says hbonds, not h-bonds, however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this. Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit = 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy = 10 nstxtcout = 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist = 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r = 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t = 0.1 ref_t = 300 Pcoupl = no Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University _zoe.h...@chem.ox.ac.uk_ Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Simulations in vacuo - energy increase
Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit= 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy= 10 nstxtcout= 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist= 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r= 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t= 0.1 ref_t= 300 Pcoupl = no Pcoupltype = Isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- 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] Simulations in vacuo
Hi gmx-users, I am trying to set up a simulation of a large protein in vacuo using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever. I am not sure, however, what is the appropriate choice for coulombtype and other electrostatic parameters for vacuum simulations. I have set epsilon_r to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it. Thanks very much, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- 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
