GROMACS version:2019

GROMACS modification: No

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Dear Gromacs users,

I have a RNA-Protein complex with a ligand with multiple chains ( about 10 chains ) , now what I want is to position restraint the atoms which are 30 Angstroms beyond that ligand.

I have tried multiple ways to generate the positional restraint files including using the the coordinates of those restraint atoms and use pdb2gmx to generate positional restraints(posre.itp) files of individual chains and include them in the main system topology but what I think is that would be a wrong way to go about doing things as these posre.itp files would have a different atom index and would possibly restrain the atoms which I wanted it to restrain in the first hand as the posre.itp file would read the heavy atoms from the topol.itp files from the corresponding chains which would have the atom index positions.

Another easy way could have been if it were a single chain protein or RNA to use genrestr but then again for my case as there are many chains in the complex generating a posre.itp file using genrestr and merely including it in my topology would lead to errors.

Could there be a easy way out to specifically restrain the desired atoms of these chains?

Here is a print out of the topol.top where I had physically added the restraint files after using pdb2gmx to generate the position restraint files which seems to be the wrong way of doing things:

```

;

; File 'topol.top' was generated

; By user: psg (1000)

; On host: pslab

; At date: Wed Aug 18 17:09:36 2021

;

; This is a standalone topology file

;

; Created by:

; :-) GROMACS - gmx pdb2gmx, 2019 (-:

;

; Executable: /usr/local/gromacs/bin/gmx

; Data prefix: /usr/local/gromacs

; Working dir: /home/psg/Desktop/new_trial

; Command line:

; gmx pdb2gmx -f rib_U_mutated.pdb -o rib.gro -ter

; Force field was read from the standard GROMACS share directory.

;

; Include forcefield parameters

#include "charmm36-mar2019_psg.ff/forcefield.itp"

; include paromomycin parameters

#include "par.prm"

; Include chain topologies

#include "topol_Ion_chain_7.itp"

#include "topol_RNA_chain_A.itp"

#include "topol_RNA_chain_A2.itp"

#include "topol_RNA_chain_a.itp"

#include "topol_RNA_chain_a2.itp"

#include "topol_RNA_chain_a3.itp"

#include "topol_RNA_chain_a4.itp"

#include "topol_RNA_chain_a5.itp"

#include "topol_RNA_chain_a6.itp"

#include "topol_Protein_chain_c.itp"

#include "topol_Protein_chain_e.itp"

#include "topol_Protein_chain_i.itp"

#include "topol_Protein_chain_k.itp"

#include "topol_Protein_chain_l.itp"

#include "topol_RNA_chain_v.itp"

#include "topol_RNA_chain_x.itp"

#include "topol_RNA_chain_y.itp"

#ifdef POSRES_RES

#include "posre_RNA_chain_A_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a2_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a3_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a4_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a5_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a6_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a7_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a8_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_a9_.itp"

#endif

#ifdef POSRES_RES

#include "posre_Protein_chain_c.itp"

#endif

#ifdef POSRES_RES

#include "posre_Protein_chain_e_.itp"

#endif

#ifdef POSRES_RES

#include "posre_Protein_chain_l_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_v_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_v2_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_x_.itp"

#endif

#ifdef POSRES_RES

#include "posre_RNA_chain_y_.itp"

#endif

; Include water topology

#include "charmm36-mar2019_psg.ff/tip3p.itp"

#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 paramomycin

#include "par.itp"

; Include topology for ions

#include "charmm36-mar2019_psg.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Ion_chain_7 1

RNA_chain_A 1

RNA_chain_A2 1

RNA_chain_a 1

RNA_chain_a2 1

RNA_chain_a3 1

RNA_chain_a4 1

RNA_chain_a5 1

RNA_chain_a6 1

Protein_chain_c 1

Protein_chain_e 1

Protein_chain_i 1

Protein_chain_k 1

Protein_chain_l 1

RNA_chain_v 1

RNA_chain_x 1

RNA_chain_y 1

PAR 1

SOL 9

SOL 67458

NA 224

```

P.S.: The chains included in POSRES_RES are those chains which were added physically by including the positional restraints file which were generated by using pdb2gmx to generate the position restraints file.(I admit this would be very wrong as it possibly read the wrong atoms and put restraint on those atoms)

It would be helpful if someone could point out where I am going wrong and help me figure a easy way out to generate the positional restraints and include them in the system topology to succesfully to restrain those particular atoms ? or could it be possible I could use the topology file (topol.top) of those restraint coordinates and not that of system topology file?

Thanking you in advance.

Regards,

Pallav