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<
http://x.86.sg/> 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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- application/octet-stream attachment: test.pdb
Received on Mon Apr 08 2024 - 12:00:02 PDT
