[gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 8:28 PM, bharat gupta wrote:
> Hi Justin,
>
> Here's the link for following files: complex.gro, CT3.itp (ligand
> topology), CT3.gro (ligand coordinates) and topology.top.
> https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA&usp=drive_web
>
> When I run make_ndx command using the solvated complex file (solv.gro), I
> don't find the ligand in any of the groups. Here's the output of that
> command:
>
> Command line:
>    make_ndx -f solv.gro -o index.ndx
>
>
> Reading structure file
> Going to read 0 old index file(s)
> Analysing residue names:
> There are:   368    Protein residues
> There are: 14227      Water residues
> Analysing Protein...
>
>    0 System              : 46221 atoms
>    1 Protein             :  3540 atoms
>    2 Protein-H           :  2746 atoms
>    3 C-alpha             :   367 atoms
>    4 Backbone            :  1101 atoms
>    5 MainChain           :  1470 atoms
>    6 MainChain+Cb        :  1795 atoms
>    7 MainChain+H         :  1826 atoms
>    8 SideChain           :  1714 atoms
>    9 SideChain-H         :  1276 atoms
>   10 Prot-Masses         :  3540 atoms
>   11 non-Protein         : 42681 atoms
>   12 Water               : 42681 atoms
>   13 SOL                 : 42681 atoms
>   14 non-Water           :  3540 atoms
>

Then solv.gro clearly doesn't contain your ligand; you haven't constructed the 
system properly.

> Also, when I ran pdb2gmx command for my protein, I got two files :
> porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
> protein chain is broken in the initial structure?
>

This just means you have multiple chains.

> For, my ligand I generated the parameters using ATB server, but the problem
> is that when I used the optimized geometry and itp files for the ligand,
> it's located far away from the active site. So, should I used the
> unoptimized geometry coordinates in that case, but wouldn't it be wrong to
> use the unoptimized geometry??
>

Do not optimize the geometry; you need the ligand's bound state to avoid such 
problems.  This issue came up in another thread just a few hours ago (it pays to 
read others' posts - quite often you'll learn something :)

-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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