[gmx-users] Protein-ligand complex energy minimization

[Indu Kumari]

Thank you Justin.

With regards,
Indu


On Tue, Aug 12, 2014 at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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