Hello everyone, I'm working on preparing my system to run MDS of 6VEI homodimer with their cocritalyzed NADPHs, I've isolated the chain A, B, NADPH A and NADPH B using Chimera software. The issue starts when I biuld the system and add coordinate the NADPH to get the .pdb and .psf file with VMD to run MDS using NAMD , here's how:

• package require psfgen
• topology top_all36_prot.rtf
• topology top_all36_cgenff1.rtf
• topology toppar_all36_na_nad_ppi.str
• pdbalias residue HIS HSE
• pdbalias atom ILE CD1 CD
• segment A {pdb 6veiA.pdb}
• coordpdb 6veiA.pdb A
• guesscoord
• segment B {pdb 6veiB.pdb}
• coordpdb 6veiB.pdb B
• guesscoord

(Until here everything works as expected and I don't get any errors)

• segment NDP_A {pdb NADPH_A.pdb}
• coordpdb NADPH_A.pdb NDP_A (here's when I get the errors)
• guesscoord

The errors are:

psfgen) reading coordinates from pdb file NADPH_A.pdb for segment NDP_A

psfgen) Warning: failed to set coordinate for atom PA NDP:601 NDP_A

psfgen) Warning: failed to set coordinate for atom O1A NDP:601 NDP_A

psfgen) Warning: failed to set coordinate for atom O2A NDP:601 NDP_A

...

I've checked with ChatGPT and it says that it could be because the NADPH_A.pdb file isn't well organized, or because the atom's order isn't as the same as the toppar_all36_na_nad_ppi.str file, or there's too much information on the NADPH_A.pdb file.

I've tried: leaving only the "HETATM" lines on the NADPH_A.pdb file; using "pdbalias residue NDP NDPH" to relate it to "RESI NDPH" (line 3522) in the toppar_all36_na_nad_ppi.str, since I tried with the "RESI NDP" (line 2627) and I got the same errors; isolating the NADPH A with PyMol and also checking the VMD manual.

I've also used the "Solution Builder" tool that's on the CHARMM-GUI web page in two ways: one was typing down the PDB code (6VEI) and the second was uploading the complex .pdb file (both times making sure to add the NADPHs), the result is the same, I get all the files but no clue of the NADPHs on the .pdb and/.psf files.

Any of these troubleshoot options have worked out, I uploaded the NADPH_A.pdb and toppar_all36_na_nad_ppi_mod.str (only deleted 5 charaters) files and thank you for your time.