[gmx-users] protein ligand simulation
bharat.85.monu at gmail.com
Wed Apr 20 02:29:20 CEST 2016
Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.
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
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
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??
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
>> 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 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
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