[gmx-users] protein ligand simulation

[bharat gupta]

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

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?

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??

Thanks

--
BM


On Tue, Apr 19, 2016 at 10:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/19/16 9:03 AM, bharat gupta wrote:
>
>> Dear Gmx users,
>>
>> I am performing a protein-ligand simulation using gromacs latest tutorial
>> for 5.0.x version. As per the tutorial, I included the coordinates of the
>> ligand in the complex.gro file (also updated total no. of atoms after
>> adding ligand atoms) and updated the topology file (topol.top) by
>> including
>> its name under the molecules sections and also included its ligand.itp
>> file. But, I am not able to find the ligand group while making an index
>> file for it. Please let me know where am I going wrong ?
>>
>>
> Well the ligand can't suddenly disappear, but in the absence of your
> actual commands and the screen output of make_ndx, there's nothing anyone
> can conclude about what the issue is.
>
> -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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