[gmx-users] Pro-lig under one molecule type

[Justin Lemkul]

On 2/18/16 12:18 AM, Sana Saeed wrote:
> hi i am working of protein ligand binding free energy calculation, i have
> seen some tutorials, like from alchemistry websites and from some paper
> works. i made ligand topology with acpype (amber.ff) and used pdb2gmx for
> protein topology, then i combined gro files to make a complex. now i dont
> know how to make complex topology. i already studies and used tutorials from
> Bevanlab but it doesnt provide info about how to include protein and ligand
> as one moleculetype. and also how should i get the dihedral, angle and
> distance restraints. i studied gromacs manual about this but it doesnt
> provide any direction. if anyone have some tutorial, kindly suggest. Thanks
> in advance
>
> ; distance restraints[ bonds ];    i     j  type     r0A     r1A     r2A
> fcA    r0B     r1B     r2B    fcB  2143  1656    10     0.615   0.615   10.0
> 0.0    0.615   0.615   10.0   4184.000 [ angle_restraints ];   ai    aj    ak
> al  type    thA      fcA    multA  thB      fcB    multB  1658  1656  2143
> 1656     1    92.14    0.0    1    92.14    41.840    1  1656  2143  2142
> 2143     1    107.4    0.0    1    107.4    41.840    1 [ dihedral_restraints
> ];   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB
> fcB  1668  1658  1656  2143     1    157.05   0.0    0.0    157.05    0.0
> 41.840  1658  1656  2143  2142     1    -129.56   0.0    0.0    -129.56
> 0.0    41.840  1656  2143  2142  2140     1    166.61   0.0    0.0    166.61
> 0.0    41.840
>

You don't need a merged [moleculetype].  To include intermolecular restraints 
and bonded terms, just use [intermolecular_interactions] at the end of the .top 
(available in versions 5.1 and newer).  Use global atom numbers to define the 
interactions.

-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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