[gmx-users] Problem running simulation on gromacs 2018.8 version

[Justin Lemkul]

On 11/8/19 7:36 AM, pooja kesari wrote:
> Dear All,
>
> I m trying to do a protein-ligand simulation,
> I am using GROMOS 43a force field, I have typed by protein and got the
> ligand file from PRODRG.

Don't use PRODRG; its topologies are not of sufficient quality for 
running MD simulations.

> I prepared the complex and added solvent. *The protein has -8.0 charge by
> when i m neutralizing it only adds 7 positive charge.*
>
>
>
> * 3328         OM    336    VAL     O1   1492     -0.635    15.9994   ;
> qtot -7.365  3329         OM    336    VAL     O2   1492     -0.635
>   15.9994   ; qtot -8*
>

Does your ligand have a +1 charge?

-Justin

> When i added 8 positive charge using  the below command
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> -np 8
>
>
>
>
>
>
>
> *[ molecules ]; Compound        #molsProtein_chain_B     11IN
>    1SOL         22473NA               8*
>
> Again in the minimization step it is showing a list of
> *errors and warnings. *
> NOTE 1 [file em.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
> Setting the LD random seed to 787146813
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> Excluding 3 bonded neighbours molecule type '1IN'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
>
> NOTE 2 [file topol.top, line 21027]:
>
> *System has non-zero total charge: 1.000000  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.
>
> WARNING 1 [file topol.top, line 21027]:
>    *You are using Ewald electrostatics in a system with net charge*. This can
>    lead to severe artifacts, such as ions moving into regions with low
>    dielectric, due to the uniform background charge. We suggest to
>    neutralize your system with counter ions, possibly in combination with a
>    physiological salt concentration.
>
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:   335    Protein residues
> There are:     1      Other residues
> There are: 22473      Water residues
> There are:     8        Ion 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 145023.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113
> Estimate for the relative computational load of the PME mesh part: 0.20
> This run will generate roughly 6 Mb of data
>
> There were 2 notes
>
> There was 1 warning
> Please suggests how can overcome these errors.

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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