[gmx-users] System with 4 Hypericin Molecules in Water

Hovakim Grabski hovakim_grabski at yahoo.com
Thu Feb 2 16:29:12 CET 2012

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?
I need your help

Thanks in advance
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