[gmx-users] The energy minimization....

of ATP as following:;    File '../ATP/ATP.top' was generated;    By user: root (0);    On host: mjduan-desktop;    At date: Wed Aug 15 16:55:53 2007;;    This is your topology file;    "Does All This Money Really Have To Go To Char ity ?" (Rick);; Include forcefield para

[gmx-users] The energy minimization....

Hi, everyone:I have meet some problem when simulating a protein and ATP complex. The energy minimization will stop after 14 steps. I had followed Mark's suggestion, did the protein and ATP eneryg minimization independently, and  found that the protein can finish its minimization correctly, but  the

[gmx-users] a problem in the energy minimization

Dear staff:When I do the energy minimization of my system contain a protein, an ATP and water molecules using mdrun, it stopped at 15 steps, and return following messeges:Steepest Descents:   Tolerance (Fmax)   =  1.0e+00   Number of steps    = 2000Step=    0, Dmax= 1.0e-02 nm, Epot= -3

[gmx-users] a problem in the energy minimization.the

Dear staff:When I do the energy minimization of my system contain a protein, an ATP and water molecules using mdrun, it stopped at 15 steps, and return this messege:Steepest Descents:   Tolerance (Fmax)   =  1.0e+00   Number of steps    = 2000Step=    0, Dmax= 1.0e-02 nm, Epot= -3.24259

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

r/ Mark Abraham wrote: > mjduan at smail.hust.edu.cn wrote: >> Dear GROMACS users: >> I want to simulate a complex composed by a protein and an ATP molecule, >> and when I use the pdb2gmx to build the topology file and transfer >> the*pdb* file to *gro* file, it sa

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

/.top file) only contain the atoms of the protein and water.) And is there any difference between the .mdp file to do grompp for this complex and for the system only contain protein and water?mjduan at smail.hust.edu.cn wrote:> Dear GROMACS users:> I want to simulate a complex composed by a pr

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Dear GROMACS users:I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer thepdb file to gro file, it said "Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms", So how can