GromacsError: Only 3-point vsite type 1 is supported

[Anis Nadyra Ahmad Zifruddin]

Hi Mario,

I've encountered another problem with other complex-ligand using CharmmFF.

Here is the error;

    raise GromacsError('Only 3-point vsite type 1 is supported')
GromacsError: Only 3-point vsite type 1 is supported

I attached my files for your reference. Thanks for your help!

[Mario Ernesto]

following this tutorial on how to proceed when the system contains LPH particles (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand_LPH_atoms_CHARMMff/)

gmx make_ndx -f step5_1.tpr -o index_mod_gromacs.ndx

>splitat 13

>13&!66

>name 67 lig

>1|67

>del 16-66

>q

should look like this

0 System              : 46744 atoms
  1 Protein             :  4002 atoms
  2 Protein-H           :  1966 atoms
  3 C-alpha             :   255 atoms
  4 Backbone            :   765 atoms
  5 MainChain           :  1019 atoms
  6 MainChain+Cb        :  1259 atoms
  7 MainChain+H         :  1263 atoms
  8 SideChain           :  2739 atoms
  9 SideChain-H         :   947 atoms
 10 Prot-Masses         :  4002 atoms
 11 non-Protein         : 42742 atoms
 12 Other               : 42742 atoms
 13 LIG                 :    51 atoms
 14 CLA                 :     4 atoms
 15 TIP3                : 42687 atoms
 16 lig                 :    50 atoms
 17 Protein_lig         :  4052 atoms

echo 17 | gmx trjconv -s step5_1.tpr -f 5frames.xtc -dump 0 -o str_noLP.pdb -n index_mod_gromacs.ndx

echo 17 | gmx trjconv -s str_noLP.pdb -f 5frames.xtc -o com_traj.pdb -n index_mod_gromacs.ndx

gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 16 -ct com_traj.pdb -cp topol.top

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[Mario Ernesto]

and use this topology for the ligand with no information about the LPH particle (see the tutorial to see how to remove the information related to LPH)