Oxygen atom of NADPH separate from molecule CHARMM36 FF

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

Dear Gromacs users,

I want to perform an MD simulation of a protein/ligand/NADPH using CHARMM36 FF. Since NADPH is in the na.rtp file obtained from MacKerell lab website (charmm36-jul2022.ff), I believed Gromacs could create the topology. So I created the ligand topology using CGENFF, added in the .gro created by pdb2gmx (protein+NADPH), created the box, and etc.

However, after the energy minimization of the complex, one of the oxygen atoms from NADPH is far from the molecule in the .gro file generated, and no error was shown by the Gromacs. Before the optimization, the atoms were in the correct positions.

In the topol.top file, there are the FF itp, ligand.prm, topol_Protein_chain.itp. topol_Other_Protein.itp (the NADPH), ligand.itp, etc. Reading the ipt Other_Protein.itp file, the only “strange” thing I could observe was the presence of 1 more atom (75) than in the na.rpt (74) for NDP…

Could someone help me to understand what’s happening?
*Yes, I know it’s a MM calculation and the break of bonds is not possible… that’s why I have no idea what’s happening

2

I think I found the error…
The .itp generated by Gromacs does not add the bonds, angles, Diedra, etc. of atom 42 (an oxygen atom). I’m trying to include it… What should I write in the [ pairs ]? I don’t understand what it is…

EDIT:
What Am I doing wrong?
I added the bond 40 42 after 40 41 (created by the Gromacs)
I added the angles 39 40 42 between 39 40 41 and 39 40 43 (…)
And the dihedrals after dihedrals with atom 41… After energy minimization, the two oxigen (41 and 42) are almost overlapping.
x y z
41 2.886 4.018 3.786
42 2.886 4.012 3.789

3

Finally… If someone has the same problem: in line 4157 of the file na.rtp (NDP) the O1N is written instead of O2N, repeating line 4156… so there are two bonds PN O1N and no PN O2N.

4

@jalemkul, is this a problem you’re aware of?

5

I met the same question,and I edit the other_chain_B.itp file,[bonds],[Angles] and [dihedrals] like follows.When i finished MD production,NADPH in md_0_10.gro looks weird.

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