I am trying to calculate binding energy between two protein using gmx_mmpbsa, but when I am running the last command to calculate binding energy (gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 19 20 -ct md_noPBC.xtc -cp topol.top), I have this error:
raise ParameterError('Not all bond parameters found')
ParameterError: Not all bond parameters found
I would appreciate if some one could help me to solve this error.
Thanks in advance
Not sure if this helps but the error message is identical with that on line 1115:
https://github.com/ParmEd/ParmEd/blob/master/parmed/gromacs/gromacstop.py
Thank you for your reply Martin,
But unfortunately I donot know how to solve this error!
Hi, what force field did you use to run the simulations? If amber FF, then remove the topol.top and see whether the error persists?
The documentation says that ParmEd is being used to convert the gmx topology to amber format. ParmeEd is tricky and usually gives errors while converting gmx to amber topology files. You need to dig deeper to find out what parameters are missing in the bond section of topol.top (or molA.itp that has been referenced in topol.top)?
Thank you Ayaz for your answer,
actually I am using GROMOS54a7 FF and this is my topol.top file:
I can not understand what bond parameters are missing. could you please help me to find out?? Thanks in advance
; File 'topol.top' was generated
; By user: unknown (1000)
; On host: DESKTOP-FHLEDG4
; At date: Sun Jun 12 23:11:53 2022
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2018.1 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /mnt/c/test
; Command line:
; gmx pdb2gmx -f model.000.00.pdb -o protein.gro -water spc
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "gromos54a7.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_A2.itp"
; Include water topology
#include "gromos54a7.ff/spc.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 ions
#include "gromos54a7.ff/ions.itp"
[ system ]
; Name
lig.000.00.pdb in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_A2 1
SOL 28899
NA 96
CL 60
Hi, I think you need to reconsider your FF choice as (from the documents):
"Currently, gmx_MMPBSA supports two families of force fields: Amber and CHARMM. Although these force fields are quite similar, the generation of topologies differs. When Amber force filed was used to prepare the system(s), the topologies compatible with AMBER package can be generated from either GROMACS topologies or structures. Meanwhile, when CHARMM force field is used, AMBER's topologies are generated from GROMACS topologies exclusively. (Table 1)."
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/howworks/
It also partially supports OPLS FF,
"PB model is recommended when working with OPLSff files. Nevertheless, the combination of PB/GB models with radii optimized for amber atom types (i.e. bondi, mbondi, mbondi2, mbondi3) and OPLS force field hasn't been tested extensively. Please, proceed with caution."
If you have already completed all the simulations, then search for another method to calculate energies, OR
Convert *.xtc and *.gro files to amber file formats and try Amber tools.
OR, You need to work with ParmEd, but it is risky and I don't recommend it.
Thank you very much Ayaz for your response,
actually the problem was force field. I used the Amber FF and did a short simulation and every thing was just fine.
you did a great help to me!!!
thanks again:)
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