After md simulation e rror in running gmx-MMPBSA for a pro-lig complex

[imren bayıl]

Hi,this my first time use gmx_MMPBSA.I applied to  md simulation for 100 ns to my complex structure which is consist of protein-ligand .After md simulation,inorder to calculate ligand binding energy kcal/mol ,I used this command,,

  gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -ci new_index.ndx -cg 1 13 -ct new.xtc -cp topol.top

my mmpbsa.in

#Sample input file for GB calculation
#This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended in the
#Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters
#according to what is better for your system.

&general
startframe=1,
endframe=1002,
keep_files=2,

/
&gb
igb=5, saltcon=0.00,
/
&pb
istrng=0.000, inp=2, radiopt=1
/

Also I attached my files

but I am getting error,

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/imren/.local/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/imren/.local/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 441, in read
    raise GromacsError('Structure contains %s molecules, but no '
GromacsError: Structure contains receptor molecules, but no template defined
Exiting. All files have been retained.

[Mario Sergio Valdes]

Sorry for the delay, I've been busy.
The problem is that ParmEd doesn't quite understand when in the [ molecules ] section of the topology the name of a molecule doesn't match its name in the [ moleculetype ] section of your itp, as happens with your receptor. In the topology, it appears as "receptor", but in the itp, it is named "PROA". Please match both names

Let me know if works for you

Mario S.

[imren bayıl]

hi,this time I couldnt change any name

gmx make_ndx -f step5.gro -o index.ndx

  0 System              : 86750 atoms
  1 Protein             :  8246 atoms
  2 Protein-H           :  4182 atoms
  3 C-alpha             :   539 atoms
  4 Backbone            :  1617 atoms
  5 MainChain           :  2155 atoms
  6 MainChain+Cb        :  2641 atoms
  7 MainChain+H         :  2646 atoms
  8 SideChain           :  5600 atoms
  9 SideChain-H         :  2027 atoms
 10 Prot-Masses         :  8246 atoms
 11 non-Protein         : 78504 atoms
 12 Other               : 78504 atoms
 13 UNK                 :    48 atoms
 14 SOD                 :     9 atoms
 15 TIP3                : 78447 atoms

 nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
 'r': residue              'res' nr         'chain' char
 "name": group             'case': case sensitive           'q': save and quit
 'ri': residue index

> q

gmx trjconv -s step5.tpr -f step5.xtc -n index.ndx -o new.xtc -pbc mol -center -ur compact

Select group for centering
Group     0 (         System) has 86750 elements
Group     1 (        Protein) has  8246 elements
Group     2 (      Protein-H) has  4182 elements
Group     3 (        C-alpha) has   539 elements
Group     4 (       Backbone) has  1617 elements
Group     5 (      MainChain) has  2155 elements
Group     6 (   MainChain+Cb) has  2641 elements
Group     7 (    MainChain+H) has  2646 elements
Group     8 (      SideChain) has  5600 elements
Group     9 (    SideChain-H) has  2027 elements
Group    10 (    Prot-Masses) has  8246 elements
Group    11 (    non-Protein) has 78504 elements
Group    12 (          Other) has 78504 elements
Group    13 (            UNK) has    48 elements
Group    14 (            SOD) has     9 elements
Group    15 (           TIP3) has 78447 elements
Select a group: 1
Selected 1: 'Protein'
Select group for output
Group     0 (         System) has 86750 elements
Group     1 (        Protein) has  8246 elements
Group     2 (      Protein-H) has  4182 elements
Group     3 (        C-alpha) has   539 elements
Group     4 (       Backbone) has  1617 elements
Group     5 (      MainChain) has  2155 elements
Group     6 (   MainChain+Cb) has  2641 elements
Group     7 (    MainChain+H) has  2646 elements
Group     8 (      SideChain) has  5600 elements
Group     9 (    SideChain-H) has  2027 elements
Group    10 (    Prot-Masses) has  8246 elements
Group    11 (    non-Protein) has 78504 elements
Group    12 (          Other) has 78504 elements
Group    13 (            UNK) has    48 elements
Group    14 (            SOD) has     9 elements
Group    15 (           TIP3) has 78447 elements
Select a group: 0
Selected 0: 'System'
Reading frame       0 time    0.000  
Precision of step5.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Last frame       1000 time 100000.000    ->  frame   1000 time 100000.000

gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -cp topol.top -ci index.ndx -cg 1 13 -ct new.xtc

[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -cp topol.top -ci index.ndx -cg 1 13 -ct new.xtc

  File "/home/imren/Downloads/amber22/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/imren/Downloads/amber22/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 440, in read

    raise GromacsError('Structure contains %s molecules, but no '

GromacsError: Structure contains UNK molecules, but no template defined

Exiting. All files have been retained.

 I am still getting error.

https://drive.google.com/drive/folders/13MFErkEphmP2CmES5KtlQQR_bz3JmYaJ?usp=sharing

22 Kasım 2022 Salı tarihinde saat 05:04:10 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

[Mario Sergio Valdes]

It is the same previous error, but with the ligand. Check the name in the topology and itp and make sure that they match

[suruchi bhambri]

i am receiving the same type of error, and is unable to understand what to do. can you pleases help me out with this?