Thanks Justin. Here is the quoted error:
processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'CL' processing coordinates... double-checking input for internal consistency... ERROR 1 [file protein.top, line 9279]: ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1104 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Three Little Fonzies" (Pulp Fiction) and the mdp ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /usr/bin/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) Hope you can locate my error here!! > Date: Wed, 17 Nov 2010 13:09:32 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error on Box Length when adding ions (gromacs > 4.5.3/Charmm27/Tip3p) > > > > X Rules wrote: > > I am having problems with grompp with my system. > > > > I am using Gromacs 4.5.3 > > FF = Charmm27 beta > > WT = TIP3P (recommended and its claimed its not too different than > > Charmms TIP3P) > > > > during minimization with pbc, I get the error about box length being > > small if I add neutralizing ions (I do not get this error in just > > water+protein system). > > > > Providing your actual sequence of commands, .mdp file(s), and the actual > (quoted) error message is the only way to diagnose what's going on. > > > Also I have tried increasing my box length upto a cube of 40 Angstroms > > and still get the error ( I have a tiny 50 residue protein). > > > > IS IT A BUG or I am doing something wrong. > > > > You're probably doing something wrong, but it's impossible to say what. > Please > provide more detail. > > -Justin > > > > > I can add more information if needed. > > > > Thanks, > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-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
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