bad atom type MN

[Gabriela Lima]

Hi guys,

I'm trying to perform MM/GBSA calculation with decomposition analysis. 

My system is a metalloprotein (Mn2+) binding to an organic small ligand.

When I use only &gb parameters, calculation works fine

&general
startframe=1912, endframe=1912,
forcefields="oldff/leaprc.ff99SBildn,leaprc.gaff"
/
&gb
igb=8,saltcon=0.150
/

However, when I add decomposition section (as below) 

&decomp
idecomp=2, dec_verbose=3,
print_res="within 10",
/

I get this error:

...

[INFO   ] Running calculations on normal system...

[INFO   ] Beginning GB calculations with /Users/GabrielaLima/Downloads/amber22/bin/sander

[INFO   ]   calculating complex contribution...

 bad atom type: MN

  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa

    app.run_mmpbsa()

  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 161, in run

    raise CalcError('%s failed with prmtop %s!' % (self.program,

CalcError: /Users/GabrielaLima/Downloads/amber22/bin/sander failed with prmtop COM.prmtop!

Exiting. All files have been retained.

It it interesting that when I use &pb parameters instead of &gb, analysis runs without this error.. 

/
&pb
istrng=0.15, fillratio=4.0,
inp=1, radiopt=0
/

It seems something related to Mn2+ parameters for GBSA decomposition analysis. Does anyone know how to solve this??

[Mario Sergio Valdes]

Hi Gabriela. Can you send me the *.mdout files?

[Gabriela Lima]

Sure! 

However, when this error occurs, only one .mdout is generated: "_GMXMMPBSA_complex_gb.mdout.0"

[Mario Sergio Valdes]

This error has already been reported on the Amber mailing list (http://archive.ambermd.org/201911/0232.html). It seems that Sander does not recognize the MN atom type, although it should have been fixed in AmberTools version 19. If possible, send me the files to my mail (*.top + *.itps, 10 frames xtc, ndx, tpr, and groups). 

[John]

Hi Guys,

Please is there any update on this. I'm encountering a similar problem with ZN2+. Interestingly, there was no issue with GPSA or PBSA analysis but running decomposition analysis gives an error as above. Please how do I resolve this? Thank you.

[Mario Sergio Valdes]

Unfortunately, this is a limitation of sander. Solve it, it is relatively complicated and requires basic programming knowledge. To include this atom, you must add to the radii definition list of the ICOSA method in sander (AmberTools22/src/sander/mdread2.F90, lines 1510-1572) this atom and then recompile the code. In your case, it should work without problems since ZN is defined unless it is not recognized as such.

[John]

Thanks, Mario, for your response. I have been trying to locate the mdread2.F90 file but to no avail. Maybe it's because I used conda installation. Also,  I made a mistake, my bad atom type was BG and not ZN. I checked my pdb and discovered no BG, but I do have Boron in my ligand, which is represented as B in the pdb file. The only place I saw BG was in the COM.prmtop file. The error I got is shown below. Please, I will appreciate your help and guidance once again. Thanks.

[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 28 residues:
R:A:VAL:25  R:A:ASN:26  R:A:TRP:28  R:A:VAL:31  R:A:PRO:32  R:A:PHE:51  R:A:HSD:77  R:A:PHE:78  R:A:HSD:79  R:A:SER:80
R:A:ASP:81  R:A:HSD:139 R:A:THR:140 R:A:CYS:158 R:A:LYS:161 R:A:LEU:165 R:A:GLY:166 R:A:ASN:167 R:A:LEU:168 R:A:GLY:169
R:A:ASP:170 R:A:ALA:171 R:A:TRP:176 R:A:SER:196 R:A:HSD:197 R::ZN2:222  R::ZN2:223  L:B:UNK:224

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 51 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 10 CPUs...

[INFO   ] Running calculations on normal system...

[INFO   ] Beginning GB calculations with /home/alaooj/anaconda3/envs/gmxMMPBSA2/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/51 [elapsed: 00:00 remaining: ?] bad atom type: BG
 bad atom type: BG
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA2/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA2/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA2/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA2/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 132, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA2/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 209, in run
    raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!')
CalcError: /home/alaooj/anaconda3/envs/gmxMMPBSA2/bin/sander failed with prmtop COM.prmtop!
Error occurred on rank 1.

Exiting. All files have been retained.

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1

Below is the part of COM.prmtop with BG 

HA2 CC  OC  OC  C   O   NH1 H   CT1 HB1 CT2 HA2 HA2 OH1 H   C   O   NH1 H   CT1
HB1 CT2 HA2 HA2 CT2 HA2 HA2 CT2 HA2 HA2 CT2 HA2 HA2 NH3 HC  HC  HC  CC  OC  OC
ZN  ZN  CG2RCG2RCG2RCG2RCG2RCG2RCG32CG31BG20OG3RSG31CG2RSG2RCG2RNG2RNG2ROG30CG2O
OG2DOG2DOG2DCG33OG2DHGR6HGR6HGA2HGA2HGA1HGR5HGA3HGA3HGA3
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA

[Mario Sergio Valdes]

Maybe it's because I used conda installation.

In this case, you need to download the AmberTools source code, change this file to include the parameter for this atom, and then compile the code. The conda installation is already compiled.

 

Could you send me your files to check them, please?

[Mario Sergio Valdes]

Your system was parameterized with CHARMM ff. In this case, the boron atom type in CHARMM is BG201, which is not recognized by Amber. It would be possible to find an equivalence for the ligand atoms, but it would take time and a lot of testing. In any case, you can use PB for this. It will take longer, but you will not have these errors. If you are going to use PB, set inp = 1 to avoid the EDISPER overstimation 

[John]

Thanks Mario, using PB worked! Thanks once again

[Andrés Álvarez]

Hi, everyone.

I have a similar problem. I want to realize a decomposition analysis of my system (heme group/myoglobin) with CHARMM force fields. However, I have the following error " bad atom type Fe" and viewing your comments is not possible to realize this analysis, or exists a form to realize it?  any strategy to follow?

• Thanks in advance.

[marioe911116]

As stated above, unfortunately, this is a limitation of sander. To include this atom, you must add to the radii definition list of the ICOSA method in sander (AmberTools22/src/sander/mdread2.F90, lines 1510-1572) this atom and then recompile the code. In this case, you need to download the AmberTools source code, change this file to include the parameter for this atom, and then compile the code.