I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each molecule are given below.
Fatal error: Syntax error - File receptor.itp, line 8 Last line read: ‘[ atomtypes ] ’ Invalid order for directive atomtypes’
My topol.top file looks like below:
; Include forcefield parameters #include “charmm27.ff/forcefield.itp”
; Include drg topology #include “DRG.itp”
; Include lig topolgy #include “LIG.itp”
; Include water topology #include “charmm27.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 ions #include “charmm27.ff/ions.itp”
[ system ] ; Name System in water
[ molecules ] ; Compound #mols LIG 1 DRG 1 SOL 6436
The two .itp files mentioned for those two molecules are attached.
It is possible that you are putting the [ atomtypes ] after having defined a molecule [ moleculetype ].
Try the following:
Take the [ atomtypes ] of your molecules and paste them in ffnonbonded.itp of your force field.
Leave in your .itp of your molecules only the ffbonded terms (everything other than Lennard-Jones parameters). You can leave the charge in your .itp [ atoms ] section,
With that gromacs will first read your
#include ffnonbonded.itpp (with your [ atomtypes ])
#influde ffbonded.itp (everything else in the force-field)
All that included in #include “charmm27.ff/forcefield.itp” (or so)
And then #include the .itp with your molecules without the [ atomtypes ]
i understand that error due to your ligand topology file. kindly re prepared as directed in Gromacs manual
Thank You, Edward, I tried the way you asked. I removed the atom types to the ffnonbonded.itp file. But then [pairtypes] error occurred. So then I moved that part to the topology section and now it only gives a warning 'too few parameters in line 7 of the DRG.itp and LIG.itp'. Thank you for your help.
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