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Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Amie Rwxayheee <ayhe1768.gmail.com>
Date: Monday, April 8, 2024 at 6:54 PM
To: Abdelrahman, Noureen <noureen.unc.edu>, AMBER Mailing List <amber.ambermd.org>, He, Amy <he.1768.buckeyemail.osu.edu>
Subject: Re: pdb4amber - Hydrogen missing in ligand!
Hi Noureen, I feel that atom H22 is likely one of the added hydrogens. I’m not very familiar with VMD usage, but a quick way to check if your parm7/rst7 contain the atoms is to load the two files in cpptraj, and do “select @H22”. If there’s
Hi Noureen,
I feel that atom H22 is likely one of the added hydrogens. I’m not very familiar with VMD usage, but a quick way to check if your parm7/rst7 contain the atoms is to load the two files in cpptraj, and do “select @H22”. If there’s a match it will return a nonempty selection.
If you want a more readable format of the prepared structure, at the end of your tleap script you can save it as a PDB for future reference.
saveAmberParm x miRFP670nano_BV_OPC.parm7 miRFP670nano_BV_OPC.rst7
savepdb x miRFP670nano_BV_OPC_initial.pdb
quit
hope this helps!
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Monday, April 8, 2024 at 5:26 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
And since H22 is in the parameters file, why does it not show up in VMD when I load my parm7 and rst7 files?
Noureen
________________________________
From: Abdelrahman, Noureen <noureen.unc.edu>
Sent: Monday, April 8, 2024 5:24 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: pdb4amber - Hydrogen missing in ligand!
Hi Amy,
Thanks for getting back to me. I checked my leap.log and I see this:
Leap added 4 missing atoms according to residue templates:
1 Heavy
3 H / lone pairs
> saveAmberParm x miRFP670nano_BV.parm7 miRFP670nano_BV.rst7
Checking Unit.
However, it does not specify H22 anywhere in the file. Is that what you mean?
Noureen
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Monday, April 8, 2024 3:21 PM
To: Abdelrahman, Noureen <noureen.unc.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: pdb4amber - Hydrogen missing in ligand!
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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 - 16:00:02 PDT