[gmx-users] Re: pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs (Tsjerk Wassenaar)

Hi Tsjerk, Thank you for your advice! grompp does not complain (with all three of the previously mentioned versions of GROMACS), but the processed topology, processed.top, also does not have the terms filled in, as I show below for the bonds section: [ bonds ] ; aiaj functc0

[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Greetings Gromacs Users, I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides. (Th

[gmx-users] classic Ewald pressure tensor

incorrect in the classic Ewald code? Sincerely, Elizabeth Ploetz ; ; File 'mdout.mdp' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Dec 23 12:23:42 2008 ; ; VARIOUS PREPROCESSING OPTIONS title= ; Preprocessor - specify a

Re: [gmx-users] GB Parameters

ecified in the mdp-file, and gets added to > the input radii for the different radii methods. > > Column 5 is the scale factor for the HCT/OBC models. The values are taken > from the original HCT reference, as well as the corresponding implementation > in Tinker. >

[gmx-users] GB Parameters

Dear Gromacs Users, I am interested in implementing implicit solvent using the OBC GBSA method.  In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file.  They all have the same co