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

[Justin A. Lemkul]

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

-- 
========================================

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

========================================