Re: [AMBER] pdb4amber - Hydrogen missing in ligand!

From: He, Amy via AMBER <amber.ambermd.org>
Date: Mon, 8 Apr 2024 19:21:43 +0000

Hi Noureen,

If H22 was added by tleap, you can see a message in leap’s log reflecting this addition. Similar to how the protonation states of histidine residues could be adjusted (from HID to HIP), hydrogens present in the residue parm files (likely the JRA.prepin in your case) can be added during system setup with tleap even if they were not present in the input PDB.

Hope this helps!

Best regards, 

--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Monday, April 8, 2024 at 2:39 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] pdb4amber - Hydrogen missing in ligand!
Hi all! I parameterized a non-standard residue (biliverdin) covalently bound to a cysteine residue by following the Amber tutorial: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue. I downloaded the .ciff file for the JRA ligand from PDB, produced the .ac file using antechamber, and my .mc file looks like this:
HEAD_NAME CAC
TAIL_NAME CAC
OMIT_NAME H27
PRE_HEAD_TYPE SG
POST_TAIL_TYPE SG
CHARGE 0.0
Per the tutorial, I used pdb4amber to reduce the molecule (protein bound to biliverdin chromophore - pdb is attached). After reducing the molecule, Biliverdin (JRA ligand) is missing hydrogen atom H22. That atom is present in the .ciff file for the JRA ligand. And I used the following tleap file to produce the parameters file:
source leaprc.protein.ff19SB
source leaprc.water.opc
loadAmberPrep JRA.prepin
loadAmberParams frcmod2.jra
loadAmberParams frcmod1.jra
x = loadPDB test.pdb
bond x.86.SG<https://urldefense.com/v3/__http://x.86.sg/__;!!KGKeukY!xFcI8MjsVFVx12OE7dhv1vXtrIt11OV31WPW8ybXkNvT-9_eiJPjg67GEu8n-ixWhSdasBgiJqnY0_umC95iYw1LIik$ > x.148.CAC
addions x Na+ 0.0
addions x Cl- 0.0
solvatebox x OPCBOX 15.0
setbox x vdw
saveAmberParm x miRFP670nano_BV_OPC.parm7 miRFP670nano_BV_OPC.rst7
quit
Weirdly enough, the parameters file also has H22. So, the H22 atom is only missing in the pdb and doesn't show in the visualizations! I did a native contacts cpptraj analysis, and H22 appeared in the native contacts output file (see a snippet of the output file below - resid 86 is the cysteine that the chromophore binds to):
1   :86.SG_:148.CAC  50000    1   1.76  0.0337
    2   :86.SG_:148.CBC  50000    1   2.68  0.0552
    3   :86.SG_:148.C3C  49897  0.998   2.83  0.0572
    4   :86.HB2_:148.CAC  49648  0.993   2.67  0.124
    5   :86.CB_:148.CAC  49636  0.993   2.81  0.0772
    6   :86.SG_:148.H22  49469  0.989   2.75  0.0993
    7    :87.N_:148.H22  49362  0.987   2.59  0.135
    8   :86.SG_:148.H29  48832  0.977   2.8  0.0937
    9   :87.HA_:148.H22  47064  0.941   2.62  0.188
   10   :56.OD2_:148.H20  46876  0.938   2.35  0.334
   11   :67.HH_:148.CGA  43236  0.865   2.71  0.156
   12    :86.C_:148.H22  42331  0.847   2.76  0.136
   13    :87.OH_:148.H2  42007   0.84   2.26  0.279
   14    :87.H_:148.H22  32493   0.65   2.76  0.165
   15   :87.CA_:148.H22  32341  0.647   2.85  0.0969
I am confused as to why that H22 appeared in the parm7 file and cpptraj analysis if it's not in the pdb. I am also wondering if it didn't get added due to a pdb4amber bug, since it is present in the ciff file. Any input would be appreciated!
Thanks,
Noureen
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Received on Mon Apr 08 2024 - 12:30:02 PDT
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