[gmx-users] The energy minimization....
http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.htmlMark:I am sorry to disturb you. I'm a beginner of GROMACS and this mailing-list system. I even don't know how to replay a post directly. And yesterday I haven't seen your replay because the list title changed, sorry again!About the problem, I haven't resolved it yet. The .top file of my ATP molecule is generated by the pdb2gmx, and the coordinates of each atom adopted to the pdb file. The force file is ffG43a2. Whether my topology file of ATP molecule have something wrong? The topology file 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 parameters#include ffG43a2.itp[ moleculetype ]; Name nrexclProtein 3[ atoms ]; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NR 1 ATP AN9 1 -0.2 14.0067 ; qtot -0.2 2 C 1 60; ATP AC4 1 0.2 12.011 ; qtot 0 3 NR 1 ATP AN3 2 -0.36 14.0067 ; qtot -0.36 4 CR1 1 ATP AC2 2 0.36 13.019 ; qtot 0 5 NR 1 ATP AN1 3 -0.36 14.0067 ; qtot -0.36 6 C 1 ATP AC6 3 0.36 12.011 ; qtot 0 7 NT 1 ATP AN6 4 -0.83 14.0067 ; qtot -0.83 8 H 1 ATP AH61 4 0.415 1.008 ; qtot -0.415 9 H 1 h
[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 ATP 's minimization stopped after 14 steps. So it seems that there are something wrong with ATP. And Mark also said Probably your topology is broken, what is it means? What should I do now?Best wishes! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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= -3.24259e+05 Fmax= 3.22275e+04, atom= 1264Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 2.96890e +04, atom= 1262Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1Double precision normally gives you higher accuracy.You might need to increase your constraint accuracy, or turnoff constraints alltogether (set constraints = none in mdp file)writing lowest energy coordinates.Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax 1.Potential Energy = -3.2425944e+05Maximum force = 3.2227543e+04 on atom 1264Norm of force = nanwhat's wrong with it? My .mdp file is:integrator = steep ;minimization methodemtol = 1.0 ; stop minimization when max force 1.0 KJ/molnsteps = 2000 ; max step numbernstenergy = 10 ;n step to write energynstxtcout = 10 ;n step to write coordinates filenstlist = 1 ;the step to update the neighbour step listns_type = simple; the method to determine neighbour listrlist = 1.0 ;cutoff for mak e neighbour listcoulombtype = cutoff ;cutoff for electrostatic force distancercoulomb = 1.0 ;long range cutoff for elect.rvdw = 1.0 ; long range cutoff for vdwconstraints = none ;no constraintpbc = no ; no periode boundary conditionsBest wishes! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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= -3.24259e+05 Fmax= 3.22275e+04, atom= 1264Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 2.96890e+04, atom= 1262Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1Double precision normally gives you higher accuracy.You might need to increase your constraint accuracy, or turnoff constraints alltogether (set constraints = none in mdp file)writing lowest energy coordinates.Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax 1.Potential Energy = -3.2425944e+05Maximum force = 3.2227543e+04 on atom 1264Norm of force = nanwhat's wrong with it? p.s. My .mdp file is:integrator = steep ;minimization methodemtol = 1.0 ; stop minimization when max force 1.0 KJ/molnsteps = 2000 ; max step numbernstenergy = 10 ;n step to write energynstxtcout = 10 ;n step to write coordinates filenstlist = 1 ;the step to update the neighbour step listns_type = simple; the method to det ermine neighbour listrlist = 1.0 ;cutoff for make neighbour listcoulombtype = cutoff ;cutoff for electrostatic force distancercoulomb = 1.0 ;long range cutoff for elect.rvdw = 1.0 ; long range cutoff for vdwconstraints = none ;no constraintpbc = no ; no periode boundary conditionsBest wishes! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to simulate a protein and a ATP molecule simultaneity?
Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.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 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 said /Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms/, So how can I build the *top* file and *gro* file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity?By reading chapter 5 of the manual thoroughly, understanding how the rtpfiles work for your force field and modifying your .pdb file and/orforce field files to work suitably.Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to simulate a protein and a ATP molecule simultaneity?
Yes, I found a server (ProDrg) can get the .gro and .top files of ATP molecule. --- Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ 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 said /Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms/, So how can I build the *top* file and *gro* file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity? By reading chapter 5 of the manual thoroughly, understanding how the rtp files work for your force field and modifying your .pdb file and/or force field files to work suitably. Mark ___ gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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 I build the top file and gro file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity?Best wishes!Mo-Jie Duan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
