[gmx-users] Charmm Sugars/carbohydrates

Hi everyone. I'm doing a simulation in gromacs using the charmm36 parameters from the gromacs website. The parameters don't seem to have carbohydrates, which are part of the charmm36 force field. In particular, I need parameters for trehalose. Is there anywhere I can find these parameters in a

Re: [gmx-users] Charge groups in Charmm for lipids

that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Cheers Tom On 06/08/11 00:22, Michael McGovern wrote: Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting i

[gmx-users] Charge groups in Charmm for lipids

Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting it together from pieces of what already exists as suggested in the charmm files.  I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology i

[gmx-users] AFM Simulation

Hi everyone. I'm doing a simulation of a system where a peptide is linked to a surface and an AFM tip is brought in contact to do force measurements. The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at various distances. Does anyone know the most direct measurement f

[gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

I'm looking for an rtp file for charmm in gromacs and according to http://www.gromacs.org/Downloads/User_contributions/Other_softwareIt should be available in a file called charmm_gromacs.tar.gz athttp://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz but the link is

[gmx-users] Re: Constraints between multiple molecules

Thanks a lot for the help, that will do well enough, but require me to redo some things I did before.  As far as you know there is no way to have multiple constraints using the center masses of the peptides?  Thanks. _One thing which you could do is to write your three proteins into one

[gmx-users] Constraints between multiple molecules

Hi everyone.  I'm doing a simulation of a protein aggregate with 3 proteins.   Ideally, I would like to constrain the distance between the center of mass of peptide 1 and the COM of peptide 2, and also constrain the distance between the combined COM of peptides 1 & 2, with the COM of peptide 3.  

[gmx-users] Charge assignment

Hi everyone.   I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6

[gmx-users] g_wham giving flat free energy

Hi everyone.  I'm having some trouble using g_wham to analyze some results.  I have some simulations from gromacs 3.3 using the pull code.  I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option.   I've gotten almost everything to work

[gmx-users] Trehalose RTP file trouble

Hi everyone.  I'm doing some simulations involving the sugar trehalose, with the 53a6 force field.  There is an odd issue I am having with the rtp file for trehalose.  It seems to be charged.  Here is the beginning of the rtp entry:  [ TRH ] [ atoms ]  HO4     H     0.41000     0   O4    OA    -0

[gmx-users] Hybrid MD-MC

Hi all.  I'm doing some simulations in gromacs and I want to include some grand canonical monte carlo steps in between runs of MD.  I want the energy calculations to be compatible with the energy calculated by gromacs.  Does anyone know a good way of doing this?Thanks. -- gmx-users mail

[gmx-users] Force between groups

Hi everyone.  I have a trajectory file and for some analysis I'm doing I need to calcualte the force between two groups of atoms.  Is there way to do this?   Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Coordinate output for test particle insertion

Hello everyone.   I'm using the test particle insertion code in gromacs, and I need the coordinates of the particle insertions for some analysis.  Unfortunately, this is not given in any output file so I need to modify the source code.  I've been trying to figure out what I need to change, but I

[gmx-users] Parameters for neutral phosho-amino acids

Hi everyone.  I'm doing some simulations of a phosphorylated peptide.  Right now, I'm using the amber force field with some parameters that were obtained for charged phosphorylated amino acids in a paper I found.  Now I want to simulate uncharged phosphate groups, but the paper only gave paramet

[gmx-users] Missing G53A6 parameters

Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I could do about that? Sho

[gmx-users] Force field problems

Hello everyone, I'm working with a peptide-like molecule that is covalently bonded to a linker. For the peptide-like part I am using a modified version of the ffG53a6 force field files. The linker section contains an alkyl section, an oligo-ethylene glycol section (...-O-CH2-CH2-O-CH2-CH2

[gmx-users] beta peptide parameters

Hello everyone. I'm trying to do a simulation involving beta peptides. There have been several papers published where parameters were developed and used. I've tried multiple times to contact the authors to get more specifics on the parameters they used, but I haven't gotten a reply. Does an