[gmx-users] System with 4 Hypericin Molecules in Water
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 2 16:35:42 CET 2012
Hovakim Grabski wrote:
> Dear GROMACS users,
> I have been trying to set up a simulation system containing 4
> Hypericin molecules in a box of water.
> When I'm trying to run energy minimization,I get this error:
> WARNING 1 [file HYP1_GMX.itp, line 5]:
> Overriding atomtype CT
> WARNING 2 [file HYP1_GMX.itp, line 6]:
> Overriding atomtype CA
> WARNING 3 [file HYP1_GMX.itp, line 7]:
> Overriding atomtype C
> WARNING 4 [file HYP1_GMX.itp, line 8]:
> Overriding atomtype O
> WARNING 5 [file HYP1_GMX.itp, line 9]:
> Overriding atomtype OH
> WARNING 6 [file HYP1_GMX.itp, line 10]:
> Overriding atomtype HA
> WARNING 7 [file HYP1_GMX.itp, line 11]:
> Overriding atomtype HO
> WARNING 8 [file HYP1_GMX.itp, line 12]:
> Overriding atomtype HC
> 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 'HYP1'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Analysing residue names:
> There are: 4 Protein residues
> There are: 5720 Water residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 52125.00
> Largest charge group radii for Van der Waals: 0.039, 0.039 nm
> Largest charge group radii for Coulomb: 0.084, 0.084 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 54x54x54, spacing 0.113 0.113 0.113
> Estimate for the relative computational load of the PME mesh part: 0.32
> This run will generate roughly 6 Mb of data
> There were 8 warnings
> I generated the topology file using acpype,after that with BallView
> copied the hypericin molecules 4 times and saved to a pdb file.
> In the topology file I made changes so that in [molecules] part,HYP1 was
> 4 (nmols) and for forcefield I included 1. #include
> "amber99sb.ff/forcefield.itp" , 2.#include "HYP1_GMX.itp" and then
> #include "amber99sb.ff/tip3p.itp".
> I didn't have any problems with setting up the system with one molecule
> of Hypericin and water box.So what was my mistake?
You're re-defining atom types that are already present in the parent force
field. The error messages indicate precisely which ones. This may or may not
present a problem, but if you're introducing new atom types (such that they do
not override global parameters for other species) then they need to have
different names (case sensitivity applies).
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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