Noureen,
to add to Amy's comments:
If I got it right, then you used the fully protonated structure
downloaded from the PDB for your parameterization, i.e. for setting up
the JRA.prepin file.
Then you used a modified (reduced) pdb to read in your actual system,
which lacks some atoms, especially H22. However, since your molecule
definition in JRA.prepin contains H22, this (and maybe other missing
atoms) is added during the leap process, when you save the parm7/rst7
file pair.
Therefore, H22 should be present both, in this file pair as well as any
pdb files derived from this pair (e.g. via ambpdb).
Thus, if you visualize your (reduced) pdb file, no H22 will be there;
but if you visualize a pdb file derived from your parm7/rst7 file pair,
the H22 should be present. Then simply inspect the pdb file with a text
editor for H22.
If the atom is not shown in VMD, you might have chosen the wrong
molecular representation for JRA: choose something like CPK or VDW to
show every atom. Note, that VMD does an automatic bond detection via a
distance cutoff in pdb files, since no bond information is present
there, so the simple lines representation might not work.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 08.04.2024 um 23:26 schrieb Abdelrahman, Noureen via AMBER:
> 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!
>
> You don't often get email from he.1768@buckeyemail.osu.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
>
> 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 Tue Apr 09 2024 - 03:00:02 PDT
