Hi Kaleem,
Your MCPB.py input file has an issue about the variable ion_ids, which should only contain the ions (not the S atoms). Delete “13436 13437 13438 13439” in the ion_ids variable could help.
Pengfei
> On Dec 4, 2023, at 9:15 PM, Kaleem Arshad via AMBER <amber.ambermd.org> wrote:
>
> Hi, AMBER Users, I am trying to generate modeling files for a mycobacterial protein containing an iron sulfur cluster. But I am facing issue that my command generates all files (small, standard, and large) except large_mk input file. Below is the shown message and my input file, Iron, and Sulfur mol2 files. Any help in this regard will be greatly appreciated.
>
> Totally there are 81 atoms in the large model.
> Totally there are 490 electrons in the large model.
> Traceback (most recent call last):
> File "/opt/amber22/bin/MCPB.py", line 651, in <module>
> gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
> File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1909, in gene_model_files
> build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly,
> File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1603, in build_large_model
> write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,
> File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mol/gauio.py", line 312, in write_gau_mkf
> raise pymsmtError("Could not find VDW parameters/radius for "
> pymsmt.exp.pymsmtError: Could not find VDW parameters/radius for element S with charge +-2
>
> software_version gms
> ion_ids 13432 13433 13434 13435 13436 13437 13438 13439
> ion_mol2files F.mol2 S.mol2
> original_pdb etfd_final.pdb
> cut_off 2.8
> force_field ff19SB
> group_name etfd
> large_opt 1
>
> .<TRIPOS>MOLECULE
> S
> 1 0 1 0 0
> SMALL
> User Assigned Charge
>
>
> .<TRIPOS>ATOM
> 13436 S 4.3400 4.3650 -5.5750 S 887 S -2.000000
> 13437 S 4.5150 5.3110 -8.3530 S 888 S -2.000000
> 13438 S 2.6920 6.6530 -6.5760 S 889 S -2.000000
> 13439 S 5.6200 6.9320 -6.1650 S 890 S -2.000000
> .<TRIPOS>BOND
> .<TRIPOS>SUBSTRUCTURE
> 1 S 1 TEMP 0 **** **** 0 ROOT
>
> .<TRIPOS>MOLECULE
> FE
> 1 0 1 0 0
> SMALL
> User Assigned Charge
>
>
> .<TRIPOS>ATOM
> 13432 FE 4.3070 7.3550 -7.7790 FE 883 FE 2.000000
> 13433 FE 3.9910 6.3520 -4.9120 FE 884 FE 2.000000
> 13434 FE 5.9580 4.9380 -6.8300 FE 885 FE 2.000000
> 13435 FE 2.9270 4.6190 -7.1210 FE 886 FE 2.000000
> .<TRIPOS>BOND
> .<TRIPOS>SUBSTRUCTURE
> 1 FE 1 TEMP 0 **** **** 0 ROOT
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Received on Wed Dec 06 2023 - 08:00:02 PST
