[gmx-users] Protein-ligand complex energy minimization

[Justin Lemkul]

On 8/12/14, 4:58 AM, Indu Kumari wrote:
> Grompp terminated and shows following warning and notes:
> NOTE 1 [file topol.top, line 57]:
>    System has non-zero total charge: -0.675997
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>

Your topology is badly broken.

>
>
> Warning: atom name 3706 in topol.top and fws_ion.pdb does not match (O1 -
> OW)
> Warning: atom name 3707 in topol.top and fws_ion.pdb does not match (P1 -
> HW1)
> Warning: atom name 3708 in topol.top and fws_ion.pdb does not match (O2 -
> HW2)
> Warning: atom name 3709 in topol.top and fws_ion.pdb does not match (O3 -
> OW)
> Warning: atom name 3710 in topol.top and fws_ion.pdb does not match (O -
> HW1)
> Warning: atom name 3711 in topol.top and fws_ion.pdb does not match (P2 -
> HW2)
> Warning: atom name 3712 in topol.top and fws_ion.pdb does not match (O5 -
> OW)
> Warning: atom name 3713 in topol.top and fws_ion.pdb does not match (O6 -
> HW1)
> Warning: atom name 3714 in topol.top and fws_ion.pdb does not match (O4 -
> HW2)
> Warning: atom name 3715 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3716 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3717 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3718 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3719 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3720 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3721 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3722 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3723 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3724 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3725 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 57]:
>    43 non-matching atom names
>    atom names from topol.top will be used
>    atom names from fws_ion.pdb will be ignored
>

The topology is also out of order with respect to the coordinate file, so any 
simulation that uses it will be totally nonsensical.  The order of [molecules] 
must exactly match that of the coordinate file, though given the nasty charge 
shown above, you have probably broken something else much earlier.

>
> Analysing residue names:
> There are:   350    Protein residues
> There are:     4      Other residues
> There are:    15        Ion residues
> There are: 21556      Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 205188.00
> Largest charge group radii for Van der Waals: 6.365, 3.730 nm
> Largest charge group radii for Coulomb:       6.365, 4.811 nm
>
> WARNING 2 [file em.mdp]:
>    The sum of the two largest charge group radii (11.176151) is larger than
>    rlist (1.000000)
>

This is either the result of having broken some molecule(s) incorrectly or may 
simply be due to PME.  Given the large charge group radii shown, I suspect the 
former.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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