I have a homodimeric protein (Chain A & B) in complex with two same ligands (LIG1 & LIG2) for MD simulation in Gromacs.
I have created separate ITP files for both ligands and the MD has completed.
But as both the Ligands are the same, I cannot create different indexes for each of them. The index LIG counts the sum of the atom number of both ligands.
Is there any way to create different individual indexes for two ligands separately?
I am not sure if I understood your question correctly but based on the atom numbers you can create two separate index files for each of your ligand.
Vishal Pandya
the problem is, as because both the ligands are same, they have same number of atoms, same atom types, same pair types (for example Lig A and Lig B both have 30 atoms each), even after creating indexes separately for Lig A and Lig B, I can see only one index LIG with 60 (30+30) atoms.
Uddipta Ghosh Dastidar, number of atoms and atom numbers are two different things. What I meant was even if you have two same ligands their atom number will be different. For instance,
LIG 1 would have atom number 1-10 and LIG-2 would have atom number from 11-20. The above information should help you index individual ligands without any issues. Once you have these ligand index files, you would be do any type of analysis you want. Moreover, you can name your ligands in your index files differently, too.
Dear Uddipta Ghosh Dastidar
As Vishal Pandya said, if you have two ligands in the systems, the in the .gro/.pdb/etc structure files you will have them both with a different name and different atom numbers. gmx make_ndx should be able to tell the difference and let you make whatever you want with the index file.
You said
I have created separate ITP files for both ligands
but also
two same ligands
Do you mean the .itp files that you #include in the topology? Then you shouldn't have two separate .itp files, because the ligands are the same. If you have thousands of water molecules, only one .itp topology for a single water molecule is needed, not thousands, as they are indeed all the same. Are you sure you have two ligands in your simulations (e.g., by looking at a VMD frame or directly at a structure file)? How did you set up the initial structure and, in particular, the topology file? Did you #include both topologies and do they have the same name and the same structure?
Best
Nicola
Nicola Piasentin , Vishal Pandya
For better understanding, I have shared the topol.top file, along with the het.itp (containing the atom types & pair types), and individual itp files of two identical ligands LIA and LIB (only their positional coordinates differ).
Should I change the atom number of each atom in LIB ?
N.B. As I wish to study the effect of each ligand separately, I do not want to add LIG 2 in [Molecules] category in topology.
Dear Uddipta Ghosh Dastidar
I am a bit confused by the topology. I suggest you follow the order of the [ molecules ] section, which is the order that must be followed in the structure file (.gro/.pdb) as well. Position restraints should be included after the molecule type they refer to, not sure why this worked? Something like
; start with forcefield params
#include "charmm27.ff/forcefield.itp"
; additional parameters for the forcefield
#include "het.itp"
; Include topology for the first ligand
#include "LIA.itp"
; ... and its restraints
#ifdef POSRES
#include "posre_LIA.itp"
#endif
; Include topology for the second ligand
#include "LIB.itp"
; ... and its restraints
#ifdef POSRES
#include "posre_LIB.itp"
#endif
; Include protein topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
; Include water topology
#include "charmm27.ff/tip3p.itp"
; ... and its restraints
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "charmm27.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
LIA 1
LIB 1
Protein_chain_A 1
Protein_chain_B 1
SOL 85630
CL 20
Your structure file has both ligands called LIG right? If that is the case, it's likely because the way you put them inside the box is that you inserted the ligand structure where the resname was LIG. You should redo from the beginning the sims, and name into the .gro/.pdb file one ligand LIA and the other LIB. Note that this will also require you to change the corresponding topologies, that is
[ moleculetype ]
; Name nrexcl
LIA 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 NPYD 1 LIG N 1 -0.5670 14.0067
2 C5B 1 LIG C 2 0.2272 12.0110
3 C5A 1 LIG C1 3 0.1054 12.0110
4 CB 1 LIG C10 4 -0.1500 12.0110
...
...
...
will become something like
[ moleculetype ]
; Name nrexcl
LIA 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 NPYD 1 LIA N 1 -0.5670 14.0067
2 C5B 1 LIA C 2 0.2272 12.0110
3 C5A 1 LIA C1 3 0.1054 12.0110
4 CB 1 LIA C10 4 -0.1500 12.0110
...
...
and the same for LIB. This will tell GROMACS that LIA and LIB are different ligands, with their given topologies LIA.itp and LIB.itp, and it should work. But, again, you will have to change the names in the structure file if they are called both just LIG.
Also a note on the restraints for the ligands. I don't really see the point of working with two different ligands, and not with two same ligands name LIG, since you can still separate them for analysis purposes. Also because you define the restraints for both ligands as
#ifdef POSRES
#include ...A or B
#endif
which means that once you activate the restraints by specifying POSRES in the .mdp file you will restrain them both at the same time. Also, note that in your .itp files for the ligands you already have the positional restraints
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
...
...
at the end of the topology, so I think you didn't need any additional "posre_LI?.itp" file. Have you tried to use the POSRES with the old topology? Seems weird you didn't get any error, since I am quite sure the [ position_restraints ] section should be included directly after the topology of the molecule to which they are referred.
Best
Nicola
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