[gmx-users] Ligand Topology file
Justin Lemkul
jalemkul at vt.edu
Tue Jan 27 18:18:59 CET 2015
On 1/27/15 3:41 AM, neha bharti wrote:
> Hello All
>
> I am performing Molecular dynamics simulation of protein and ligand
> complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
> am using Automated topology builder.
> In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
> ions.tpr) when I tried to add ion it gives me Note that
>
> NOTE 2 [file topol.top]:
> The largest charge group contains 14 atoms.
> Since atoms only see each other when the centers of geometry of the charge
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
>
> Following is the atom charge group of .itp file which I get from Automated
> topology builder
>
>
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass total_charge
> 1 C 1 6P5P C15 1 -0.050 12.0110
> 2 C 1 6P5P C16 1 0.023 12.0110
> 3 C 1 6P5P C17 1 0.023 12.0110
> 4 C 1 6P5P C18 1 -0.050 12.0110
> 5 C 1 6P5P C19 1 0.023 12.0110
> 6 C 1 6P5P C20 1 0.023 12.0110
> 7 C 1 6P5P C14 1 0.580 12.0110
> 8 O 1 6P5P O1 1 -0.571 15.9994
> 9 C 1 6P5P C21 1 0.570 12.0110
> 10 O 1 6P5P O2 1 -0.571 15.9994 ; 0.000
> 11 N 1 6P5P N3 2 -0.486 14.0067
> 12 H 1 6P5P H11 2 0.486 1.0080 ; 0.000
> 13 C 1 6P5P C12 3 0.251 12.0110
> 14 C 1 6P5P C11 3 -0.019 12.0110
> 15 C 1 6P5P C10 3 -0.070 12.0110
> 16 C 1 6P5P C9 3 0.089 12.0110
> 17 C 1 6P5P C8 3 -0.185 12.0110
> 18 C 1 6P5P C13 3 -0.089 12.0110
> 19 C 1 6P5P C7 3 0.491 12.0110
> 20 NR 1 6P5P N2 3 -0.468 14.0067 ; -0.000
> 21 NR 1 6P5P N1 4 -0.365 14.0067
> 22 H 1 6P5P H1 4 0.365 1.0080 ; 0.000
> 23 C 1 6P5P C5 5 0.155 12.0110
> 24 C 1 6P5P C4 5 0.115 12.0110
> 25 C 1 6P5P C6 5 -0.042 12.0110
> 26 C 1 6P5P C3 5 -0.042 12.0110
> 27 C 1 6P5P C2 5 -0.093 12.0110
> 28 C 1 6P5P C1 5 -0.093 12.0110 ; 0.000
> 29 N 1 6P5P N4 6 -0.486 14.0067
> 30 H 1 6P5P H16 6 0.486 1.0080 ; 0.000
> 31 C 1 6P5P C22 7 0.240 12.0110
> 32 C 1 6P5P C27 7 -0.100 12.0110
> 33 C 1 6P5P C26 7 -0.196 12.0110
> 34 C 1 6P5P C25 7 0.078 12.0110
> 35 C 1 6P5P C24 7 -0.081 12.0110
> 36 C 1 6P5P C23 7 -0.030 12.0110
> 37 C 1 6P5P C28 7 0.478 12.0110
> 38 NR 1 6P5P N6 7 -0.475 14.0067
> 39 C 1 6P5P C34 7 0.138 12.0110
> 40 C 1 6P5P C29 7 0.170 12.0110
> 41 C 1 6P5P C33 7 -0.030 12.0110
> 42 C 1 6P5P C30 7 -0.030 12.0110
> 43 C 1 6P5P C31 7 -0.081 12.0110
> 44 C 1 6P5P C32 7 -0.081 12.0110 ; 0.000
> 45 NR 1 6P5P N5 8 -0.365 14.0067
> 46 H 1 6P5P H2 8 0.365 1.0080 ; 0.000
> ; total charge of the molecule: -0.000
>
>
>
> Should I ignore the error or is there something wrong in my charge group
> generated from ATB.
> Can any one please help me out to solve the problem.
>
There are several charge groups that are too large, and group 7 is the one that
is triggering the problem. Note that charge groups are only relevant for the
group cutoff scheme, and are ignored with Verlet. Scrutinize all elements of
the topology; if something as fundamental as the charge groups (which should
only ever encompass 2-4 atoms based on chemical moiety) are this bizarre, likely
the charges are suboptimal, as well.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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