Hi Rubha,

I am assuming that you are using the latest version of charmm36m and your input file for pdbtogmx is in PDB format.

If you open the corresponding merged.rtp file of the charmm36m force field and search for the NAD entry, you will see that it expects the phosporatoms to be named as follows (highlighted in bold below):

P2B

PA

PN

As there is no definition for a P1 atom in the rtp file, you need to rename your atoms in the input file to match the format in the rtp file. I have attached the full NDP definition for you at the end.

Good luck!

[ NDP ]

[ atoms ]

C4B CN7 0.160 0

H4B HN7 0.090 1

O4B ON6B -0.500 2

C1B CN7B 0.160 3

H1B HN7 0.090 4

C5A CN5 0.280 5

N7A NN4 -0.710 6

C8A CN4 0.340 7

H8A HN3 0.120 8

N9A NN2 -0.050 9

N1A NN3A -0.740 10

C2A CN4 0.500 11

H2A HN3 0.130 12

N3A NN3A -0.750 13

C4A CN5 0.430 14

C6A CN2 0.460 15

N6A NN1 -0.770 16

H61A HN1 0.380 17

H62A HN1 0.380 18

C2B CN7B 0.010 19

H2B HN7 0.090 20

O2B ON2 -0.620 21

P2B P 1.500 22

O1X ON3 -0.820 23

O2X ON3 -0.820 24

O3X ON4 -0.680 25

HO2A HN4 0.340 26

C3B CN7 0.140 27

H3B HN7 0.090 28

O3B ON5 -0.660 29

HO3A HN5 0.430 30

C5B CN8B -0.080 31

H51A HN8 0.090 32

H52A HN8 0.090 33

PA P 1.500 34

O1A ON3 -0.820 35

O2A ON3 -0.820 36

O5B ON2 -0.620 37

O3 ON2 -0.680 38

PN P 1.500 39

O1N ON3 -0.820 40

O2N ON3 -0.820 41

O5D ON2 -0.620 42

C5D CN8B -0.080 43

H51N HN8 0.090 44

H52N HN8 0.090 45

C2D CN7B 0.140 46

H2D HN7 0.090 47

O2D ON5 -0.660 48

HO2N HN5 0.430 49

C3D CN7 0.140 50

H3D HN7 0.090 51

O3D ON5 -0.660 52

HO3N HN5 0.430 53

C1D CN7B 0.160 54

H1D HN7 0.090 55

C4D CN7 0.160 56

H4D HN7 0.090 57

O4D ON6B -0.500 58

N1N NN2 -0.270 59

C6N CN3C -0.060 60

HN6 HN6 0.170 61

C5N CN3 -0.180 62

H5N HN6 0.140 63

C4N CN8 -0.280 64

H41N HN8 0.090 65

H42N HN8 0.090 66

C3N CN3 0.360 67

C2N CN3C -0.100 68

H2N HN6 0.140 69

C7N CN1A 0.550 70

O7N ON1 -0.510 71

N7N NN1 -0.720 72

H71N HN1 0.260 73

H72N HN1 0.320 74

[ bonds ]

N1A C2A

N3A C4A

C5A C6A

C6A N6A

C5A N7A

C8A N9A

N9A C4A

C2A H2A

N6A H61A

N6A H62A

C8A H8A

N9A C1B

C1B C2B

C2B C3B

C3B C4B

C4B O4B

O4B C1B

C1B H1B

C2B O2B

O2B P2B

C2B H2B

C3B H3B

C3B O3B

O3B HO3A

C4B H4B

C4B C5B

C5B H52A

C5B H51A

C5B O5B

O5B PA

PA O1A

PA O2A

PA O3

O3 PN

PN O1N

PN O1N

PN O5D

O5D C5D

C5D H51N

C5D H52N

C5D C4D

C4D O4D

O4D C1D

C1D C2D

C2D C3D

C3D C4D

C1D H1D

C2D H2D

C2D O2D

O2D HO2N

C3D H3D

C3D O3D

O3D HO3N

C4D H4D

C1D N1N

N1N C2N

C3N C4N

C5N C6N

C2N H2N

C3N C7N

C7N O7N

C7N N7N

N7N H71N

N7N H72N

C4N H41N

C4N H42N

C5N H5N

C6N HN6

P2B O1X

P2B O2X

P2B O3X

O3X HO2A

C6A N1A

C2A N3A

C4A C5A

N7A C8A

C2N C3N

C4N C5N

C6N N1N

[ impropers ]

N6A C6A H61A H62A

C6A N1A C5A N6A

C7N N7N C3N O7N

C7N C3N N7N O7N

N7N C7N H71N H72N

N7N C7N H72N H71N

C6N N1N C5N HN6

C5N C6N C4N H5N

C4N C5N C3N H41N

C2N C3N N1N H2N

Thank for reply ,@Tobias

Now Again i am getting error after running the command

"gmx_mpi grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr"

the error is

ERROR 1 [file UNK.prm, line 71]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 2 [file UNK.prm, line 72]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

can anyone help in rectifying this error

HiRubha,

could you please share the UNK.prm + topol.top file, then it is much easier to see what did not work properly.

Thank you so much for response Tobias Rindfleisch

I have rectified that error,

But I have one another query regarding Protein ligand Complex MDS

If complex contains two Hetatoms i.e. NDP and UNK, interacting with Protein .What is the procedure for MDS using gromacs. Whether we have to create topology file for both NDP and UNK and merge it with Protein? or some other procedure is there?

Kindly give suggestion...

Hi Rubha,

if you want to use more than one ligand, you need to include the corresponding itp file(s) in your topol.top file, via

#include ligand_1.itp

#include ligand_2.itp

if they are not already included directly.

Thank you for your suggestion Tobias Rindfleisch

Now i want to know how to perform MMPBSA for this complex having two hetatoms, NDP and UNK?

when i have tried "gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200_final.tpr -ct final_10ns.xtc -ci index.ndx -cg 1 14 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv" cpmmand

i got error

Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained.

(gmxMMPBSA_final) [root@skslabp10001 Cocrystal]# cd

(gmxMMPBSA_final) [root@skslabp10001 ~]# cd D

Desktop/ Documents/ Downloads/

(gmxMMPBSA_final) [root@skslabp10001 ~]# cd Desktop/

(gmxMMPBSA_final) [root@skslabp10001 Desktop]# cdr

cdrdao cdrecord

(gmxMMPBSA_final) [root@skslabp10001 Desktop]# cd /home/skslab/Desktop/Rubha/Rubha/Collab/Velmurugan/Antifungal

(gmxMMPBSA_final) [root@skslabp10001 Antifungal]# cd 8_hydroxyflavone/

(gmxMMPBSA_final) [root@skslabp10001 8_hydroxyflavone]# gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200_final.tpr -ct final_10ns.xtc -ci index.ndx -cg 1 14 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO ] Starting gmx_MMPBSA v1.6.2

[INFO ] Command-line

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200_final.tpr -ct final_10ns.xtc -ci index.ndx -cg 1 14 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

tets

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

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

[INFO ] Checking external programs...

[INFO ] cpptraj found! Using /home/skslab/miniconda3/envs/gmxMMPBSA_final/bin/cpptraj

[INFO ] tleap found! Using /home/skslab/miniconda3/envs/gmxMMPBSA_final/bin/tleap

[INFO ] parmchk2 found! Using /home/skslab/miniconda3/envs/gmxMMPBSA_final/bin/parmchk2

[INFO ] sander found! Using /home/skslab/miniconda3/envs/gmxMMPBSA_final/bin/sander

[INFO ] Using GROMACS version > 5.x.x!

[INFO ] gmx found! Using /home/skslab/miniconda3/envs/gmxMMPBSA_final/bin.AVX2_256/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 Protein_UNK (1_14) 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 Protein (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 UNK (14) 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...

[INFO ] Detected CHARMM force field topology format...

[INFO ] Assigning PBRadii mbondi2 to Complex...

[INFO ] Writing Normal Complex AMBER topology...

[INFO ] No Receptor topology file was defined. Using ST approach...

[INFO ] Building AMBER Receptor topology from Complex...

[INFO ] Assigning PBRadii mbondi2 to Receptor...

[INFO ] Writing Normal Receptor AMBER topology...

[INFO ] No Ligand topology file was defined. Using ST approach...

[INFO ] Building AMBER Ligand topology from Complex...

[INFO ] Assigning PBRadii mbondi2 to Ligand...

[INFO ] Writing Normal Ligand AMBER topology...

[WARNING] Number of decomp residues to print using print_res = 'within 6' < 2

[INFO ] Increasing cutoff value by 0.1 until number of decomp residues to print >= 2

[ERROR ] MMPBSA_Error

The maximum number of iterations to select interaction residues was reached. Please set print_res with a valid selection.

Check the gmx_MMPBSA.log file to report the problem.

File "/home/skslab/miniconda3/envs/gmxMMPBSA_final/bin/gmx_MMPBSA", line 8, in

sys.exit(gmxmmpbsa())

File "/home/skslab/miniconda3/envs/gmxMMPBSA_final/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa

app.make_prmtops()

File "/home/skslab/miniconda3/envs/gmxMMPBSA_final/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops

self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

File "/home/skslab/miniconda3/envs/gmxMMPBSA_final/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 146, in buildTopology

GMXMMPBSA_ERROR('The maximum number of iterations to select interaction residues was '

File "/home/skslab/miniconda3/envs/gmxMMPBSA_final/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__

raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')

MMPBSA_Error:

The maximum number of iterations to select interaction residues was reached. Please set print_res with a valid selection.

Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained.

How to rectify this?

Hi Rubha,

I don't have any experience with MMPBSA, so unfortunately I can't help you any further. But good luck and success!

Thanks for all your suggestion Tobias Rindfleisch

I will try and resolve it soon

Thanks again!!