Help, adding PEG to my gro and top file-is not placed where it should be

User discussions
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1

GROMACS version: :-) GROMACS - gmx editconf, 2022.4 (-:
GROMACS modification: Yes/No
Hello Gromacs community,

I am trying to run an implicit solvation on a complex with two proteins, two glycan, and two PEG. I have successfully created a topol.top and conf.gro for the protein and glycans. The PEGs are however large. I followed the protein-ligand tutorial, took individual PEGs and converted to mol2 and ran through CGenFF. I took the UNK_gmx.pdb and UNL_gmx.pdb generated from CGenFF and converted to gro and added to my gro file and corrected the number of atoms. Then from the top files created the itps and added to my top file (protein/glycan):
Command line:
; gmx pdb2gmx -f Fc_Pert_1K_delH.pdb -o conf.gro
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include “./charmm36-jul2022.ff/forcefield.itp”

; Include chain topologies
#include “topol_Other_chain_C.itp”
#include “topol_Other_chain_D.itp”
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.itp”

; Include PEG topologies
#include “UNK.itp”
#include “UNL.itp”

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Other_chain_C 1
Other_chain_D 1
Protein_chain_A 1
Protein_chain_B 1
UNK 1
UNL 1

But when I open the gro file, the PEGs are not in the right position like how I have them in the original PDB file, which they are covalently bonded to the glycans. Can someone help me please?

NOTE: I have also tried editconf with the converted gro PEG files to the box dimensions that are in the original protein/glycan gro file, but that made it worse.

All is appreciated, thank you,

Heather

2

In order to get them in the right place you will need to retain the original coordinates and system dimensions.

There are probably many ways to do this, but one way would be to create an index file from your original PDB file and then extract the PEGs, from the PDB file, to a separate .gro file using gmx editconf with your index file as -n option. Then you can add the contents of that .gro file to the end of the gro file with the protein and glycans. Hopefully that will work fine.

3

Thank you, I ran it through a sort_bond code and it corrected it before I added to the CGenFF. This did work for my system. When I was doing further research on this, do you know if implicit solvation is still available on Gromacs? Or if there is another way to do such. My system is localized and am trying to run free energy calculations for it. Thank you

4

If you want to run free energy calculations in implicit solvent it’s possible that g_mmpbsa might be of interest. Have a look at the references and see if it’s of use. I’ve never tried it myself.

But in general, implicit solvent simulations as such are not available in GROMACS at the moment.