[gmx-users] Ligand and ion topology

[Justin Lemkul]

On 7/4/17 5:33 AM, Khadija Amine wrote:
> Dear gromacs users,
> 
> I have a protein with GNP ligand and acetate ACT ion that I want to
> simulate.
> 
> I have prepared topologies for both GNP and ACT with PRODRG program.
> 

Don't use PRODRG unless you manually reparametrize the charges and charge groups 
afterward.

> My first question is: Where should I exactly include the ACT.itp and
> GNP.itp into topol.top file?
> 

In principle, anywhere after the initial force field #include statement, as long 
as no new parameter types are introduced.

> My second question is:
> I have Copied and pasted the coordinates from my two molecules files onto
> the end of the protein.gro file. I have changed the number at the top or
> beginning of the file from as it should be to corrected the total number of
> atoms in the file.
> 
> Should I change the atom number column and renumber the atoms with the new
> ones?
> 

mdrun doesn't care about coordinate file numbering.

> Is this will affect the position of the ligand and the ions in the protein
> structure?
> 

Only coordinates affect positions, not atom numbers.

-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

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