Help Needed to Generate Topology File for Glutamate and Chlorophyll A System

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Dear Gromacs use
Dear GROMACS Community,

I am currently working on a project that involves investigating the binding between glutamate and chlorophyll A. To achieve this, I have prepared the ITP files for both glutamate and chlorophyll A. However, I am facing difficulties in generating the combined topology (.top) file for the system.

Here is what I have done so far:

  1. Prepared the structure files for both glutamate and chlorophyll A.
  2. Created individual ITP files for both molecules.
  3. Tried to combine them into a single system topology file.

I attempted to create a combined topol.top file as follows:
acpype_newbondCLAGLU.top (74.5 KB)

Despite following these steps, I am encountering issues when trying to generate the topology file. I am not sure if there are errors in my ITP files or if I am missing some steps.

Could anyone please provide guidance or suggest corrections? Any help on how to correctly format and combine these files would be greatly appreciated.

Thank you in advance for your assistance!

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Please provide terminal output to analyze error.

1 Like
3

Hello hemantaup and thank you for your help.

ERROR 1 [file acpype_newbondCLAGLU.top, line 266]:
Atom index (98) in bonds out of bounds (1-97).
This probably means that you have inserted topology section “bonds”
in a part belonging to a different molecule than you intended to.
In that case move the “bonds” section to the right molecule.

There were 2 notes
Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1948)

Fatal error:
There was 1 error in input file(s)

4

I think, there is a better way to solve this issue. If you have .itp file for each molecules then you just place it in your working directory. Now you manually edit your topology file.

#include "amber99sb-ildn.ff/forcefield.itp"
#include "./GLUTAMATE.itp"
#include "./CHLOROPHYLL.itp"
; Replace with your .itp name



; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

;place posre.itp in your working directory
 
; Include water topology
#include "amber99sb-star-ildnp.ff/spce.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 "amber99sb-star-ildnp.ff/ions.itp"


[ system ]
; Name
Glutamate and Chlorophyll A

[ molecules ]
; Compound        #mols
CLA_GLU           1  
; replace with suitable no of molecules and name of molecule. This number should exactly match the number of molecule in your system

Note: One problem may still arise due to atomtype. To remove this issue you just cut both atom type section and paste in a single atomtype.itp file and include just below forcefield.itp
Tips: To Check number of molecule you can use:

gmx make_ndx your_file.gro
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5

Thank you very much for your help.

I actually modified as you explained, but unfortunately, I had the error as you expected. Then I generated the atomtype.itp files for both glutamate and chlorophyll after executing this command:
gmx grompp -f opt1.mdp -c complex.gro -p acpype_newbondCLAGLU.top -o complex.tpr
I had this error:
Fatal error:
Syntax error - File CLA_GMX.itp, line 1
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes
please see below top file after modifications:
acpype_newbondCLAGLU.top (71.8 KB)

6

Try this one:
acpype_newbondCLAGLU(1).top (1.5 KB)

If this doesn’t work, please provide me individual itp files, also gro file (if you don’t mind).

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7

Also it didnot work and had this error :
Fatal error:
Syntax error - File CLA_GMX.itp, line 1
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes
Please find the attached files
CLA_GMX.itp.txt (97.1 KB)
glu_GMX.itp.txt (9.1 KB)
complex.gro.txt (10.6 KB)
Please note that I have changed just the formate to .txt in order to upload it here.

8

complex.gro.txt (6.8 KB)
here is the corrected gro file

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Check with these files:
acpype_newbondCLAGLU.top (639 Bytes)
atom_type.itp.txt (2.9 KB)
glu_GMX.itp.txt (8.3 KB)
CLA_GMX.itp.txt (94.9 KB)

Note: All itp files are modified (atom type removed and added to atom_type.itp). So, use all these files.

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10

Dear hemantaup,
I used them and I had this error :
Fatal error:
Topology include file “amber99sb-star-ildnp.ff/spce.itp” not found.
inspite of that I have this forcefield in my directory.

11

Dear Hemantaup,
First of all, I would like to thank you for your help and your time. Your guidance was helpful, and it worked successfully. Now I can move forward to the next steps.

1 Like
12

Hi,
Here the updates for my project , the simulation ran without any errors, and the process completed successfully. However, upon visual inspection via VMD of the resulting boxed.gro file, I noticed that the structure appears incorrect.
Please find the attached below.
boxed.gro.txt (6.9 KB)
complex.gro.txt (6.8 KB)

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Hi @Raeed83 I am facing problem in generating the topology of chlorophyll A due to Mg. How you generated the topology. In addition which forcefield in Gromacs you used. I am using Gromacs 2020.5 Version.