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