Can anyone please tell me why amber is adding new atoms and missing heavy
atoms in the protein molecule, even if PDB file contains no missing
residues?? I have imported protein- RNA complex into amber using forcefield
"leaprc.ff14SB" and ion parameter file " frcmod.ionsjc_tip3p". After
loading pdb into xleap using command "prot = loadpdb "4egl7f1.pdb" I'm
getting this message
> prot = loadpdb "let7f1dock.pdb"
Loading PDB file: ./let7f1dock.pdb
(starting new molecule for chain B)
Created a new atom named: HT1 within residue: .R<NGLY 18>
Created a new atom named: HT2 within residue: .R<NGLY 18>
Created a new atom named: HT3 within residue: .R<NGLY 18>
Created a new atom named: HN within residue: .R<ARG 19>
Created a new atom named: HN within residue: .R<THR 20>
Created a new atom named: HN within residue: .R<ASN 21>
Created a new atom named: HN within residue: .R<LEU 22>
Created a new atom named: HN within residue: .R<ILE 23>
Created a new atom named: HN within residue: .R<VAL 24>
Created a new atom named: HN within residue: .R<ASN 25>
Created a new atom named: HN within residue: .R<TYR 26>
Created a new atom named: HN within residue: .R<LEU 27>
Created a new atom named: HN within residue: .R<GLN 29>
Created a new atom named: HN within residue: .R<ASN 30>
Created a new atom named: HN within residue: .R<MET 31>
Created a new atom named: HN within residue: .R<THR 32>
Created a new atom named: HN within residue: .R<GLN 33>
Created a new atom named: HN within residue: .R<ASP 34>
Created a new atom named: HN within residue: .R<GLU 35>
Created a new atom named: HN within residue: .R<LEU 36>
Created a new atom named: HN within residue: .R<ARG 37>
Created a new atom named: HN within residue: .R<SER 38>
Created a new atom named: HN within residue: .R<LEU 39>
Created a new atom named: HN within residue: .R<PHE 40>
Created a new atom named: HN within residue: .R<SER 41>
Created a new atom named: HN within residue: .R<SER 42>
Created a new atom named: HN within residue: .R<ILE 43>
Created a new atom named: HN within residue: .R<GLY 44>
Created a new atom named: HN within residue: .R<GLU 45>
Created a new atom named: HN within residue: .R<VAL 46>
Created a new atom named: HN within residue: .R<GLU 47>
Created a new atom named: HN within residue: .R<SER 48>
Created a new atom named: HN within residue: .R<ALA 49>
Created a new atom named: HN within residue: .R<LYS 50>
Created a new atom named: HN within residue: .R<LEU 51>
Created a new atom named: HN within residue: .R<ILE 52>
Created a new atom named: HN within residue: .R<ARG 53>
Created a new atom named: HN within residue: .R<ASP 54>
Created a new atom named: HN within residue: .R<LYS 55>
Created a new atom named: HN within residue: .R<VAL 56>
Created a new atom named: HN within residue: .R<ALA 57>
Created a new atom named: HN within residue: .R<GLY 58>
Created a new atom named: HN within residue: .R<HIE 59>
Created a new atom named: HN within residue: .R<SER 60>
Created a new atom named: HN within residue: .R<LEU 61>
Created a new atom named: HN within residue: .R<GLY 62>
Created a new atom named: HN within residue: .R<TYR 63>
Created a new atom named: HN within residue: .R<GLY 64>
Created a new atom named: HN within residue: .R<PHE 65>
Created a new atom named: HN within residue: .R<VAL 66>
Created a new atom named: HN within residue: .R<ASN 67>
Created a new atom named: HN within residue: .R<TYR 68>
Created a new atom named: HN within residue: .R<VAL 69>
Created a new atom named: HN within residue: .R<THR 70>
Created a new atom named: HN within residue: .R<ALA 71>
Created a new atom named: HN within residue: .R<LYS 72>
Created a new atom named: HN within residue: .R<ASP 73>
Created a new atom named: HN within residue: .R<ALA 74>
Created a new atom named: HN within residue: .R<GLU 75>
Created a new atom named: HN within residue: .R<ARG 76>
Created a new atom named: HN within residue: .R<ALA 77>
Created a new atom named: HN within residue: .R<ILE 78>
Created a new atom named: HN within residue: .R<ASN 79>
Created a new atom named: HN within residue: .R<THR 80>
Created a new atom named: HN within residue: .R<LEU 81>
Created a new atom named: HN within residue: .R<ASN 82>
Created a new atom named: HN within residue: .R<GLY 83>
Created a new atom named: HN within residue: .R<LEU 84>
Created a new atom named: HN within residue: .R<ARG 85>
Created a new atom named: HN within residue: .R<LEU 86>
Created a new atom named: HN within residue: .R<GLN 87>
Created a new atom named: HN within residue: .R<SER 88>
Created a new atom named: HN within residue: .R<LYS 89>
Created a new atom named: HN within residue: .R<THR 90>
Created a new atom named: HN within residue: .R<ILE 91>
Created a new atom named: HN within residue: .R<LYS 92>
Created a new atom named: HN within residue: .R<VAL 93>
Created a new atom named: HN within residue: .R<SER 94>
Created a new atom named: HN within residue: .R<TYR 95>
Created a new atom named: HN within residue: .R<ALA 96>
Created a new atom named: HN within residue: .R<ARG 97>
Created a new atom named: HN within residue: .R<SER 99>
Created a new atom named: HN within residue: .R<SER 100>
Created a new atom named: HN within residue: .R<GLU 101>
Created a new atom named: HN within residue: .R<VAL 102>
Created a new atom named: HN within residue: .R<ILE 103>
Created a new atom named: HN within residue: .R<LYS 104>
Created a new atom named: HN within residue: .R<ASP 105>
Created a new atom named: HN within residue: .R<ALA 106>
Created a new atom named: HN within residue: .R<ASN 107>
Created a new atom named: HN within residue: .R<LEU 108>
Created a new atom named: HN within residue: .R<TYR 109>
Created a new atom named: HN within residue: .R<ILE 110>
Created a new atom named: HN within residue: .R<SER 111>
Created a new atom named: HN within residue: .R<GLY 112>
Created a new atom named: HN within residue: .R<LEU 113>
Created a new atom named: HN within residue: .R<ARG 115>
Created a new atom named: HN within residue: .R<THR 116>
Created a new atom named: HN within residue: .R<MET 117>
Created a new atom named: HN within residue: .R<THR 118>
Created a new atom named: HN within residue: .R<GLN 119>
Created a new atom named: HN within residue: .R<LYS 120>
Created a new atom named: HN within residue: .R<ASP 121>
Created a new atom named: HN within residue: .R<VAL 122>
Created a new atom named: HN within residue: .R<GLU 123>
Created a new atom named: HN within residue: .R<ASP 124>
Created a new atom named: HN within residue: .R<MET 125>
Created a new atom named: HN within residue: .R<PHE 126>
Created a new atom named: HN within residue: .R<SER 127>
Created a new atom named: HN within residue: .R<ARG 128>
Created a new atom named: HN within residue: .R<PHE 129>
Created a new atom named: HN within residue: .R<GLY 130>
Created a new atom named: HN within residue: .R<ARG 131>
Created a new atom named: HN within residue: .R<ILE 132>
Created a new atom named: HN within residue: .R<ILE 133>
Created a new atom named: HN within residue: .R<ASN 134>
Created a new atom named: HN within residue: .R<SER 135>
Created a new atom named: HN within residue: .R<ARG 136>
Created a new atom named: HN within residue: .R<VAL 137>
Created a new atom named: HN within residue: .R<LEU 138>
Created a new atom named: HN within residue: .R<VAL 139>
Created a new atom named: HN within residue: .R<ASP 140>
Created a new atom named: HN within residue: .R<GLN 141>
Created a new atom named: HN within residue: .R<THR 142>
Created a new atom named: HN within residue: .R<THR 143>
Created a new atom named: HN within residue: .R<GLY 144>
Created a new atom named: HN within residue: .R<LEU 145>
Created a new atom named: HN within residue: .R<SER 146>
Created a new atom named: HN within residue: .R<ARG 147>
Created a new atom named: HN within residue: .R<GLY 148>
Created a new atom named: HN within residue: .R<VAL 149>
Created a new atom named: HN within residue: .R<ALA 150>
Created a new atom named: HN within residue: .R<PHE 151>
Created a new atom named: HN within residue: .R<ILE 152>
Created a new atom named: HN within residue: .R<ARG 153>
Created a new atom named: HN within residue: .R<PHE 154>
Created a new atom named: HN within residue: .R<ASP 155>
Created a new atom named: HN within residue: .R<LYS 156>
Created a new atom named: HN within residue: .R<ARG 157>
Created a new atom named: HN within residue: .R<SER 158>
Created a new atom named: HN within residue: .R<GLU 159>
Created a new atom named: HN within residue: .R<ALA 160>
Created a new atom named: HN within residue: .R<GLU 161>
Created a new atom named: HN within residue: .R<GLU 162>
Created a new atom named: HN within residue: .R<ALA 163>
Created a new atom named: HN within residue: .R<ILE 164>
Created a new atom named: HN within residue: .R<THR 165>
Created a new atom named: HN within residue: .R<SER 166>
Created a new atom named: HN within residue: .R<PHE 167>
Created a new atom named: HN within residue: .R<ASN 168>
Created a new atom named: HN within residue: .R<GLY 169>
Created a new atom named: HN within residue: .R<HIE 170>
Created a new atom named: HN within residue: .R<LYS 171>
Created a new atom named: OXT within residue: .R<LYS 171>
Created a new atom named: HT1 within residue: .R<GLY 172>
Created a new atom named: HT2 within residue: .R<GLY 172>
Created a new atom named: HT3 within residue: .R<GLY 172>
Created a new atom named: HN within residue: .R<SER 173>
Created a new atom named: HN within residue: .R<SER 174>
Created a new atom named: HN within residue: .R<GLU 175>
Created a new atom named: HN within residue: .R<ILE 177>
Created a new atom named: HN within residue: .R<THR 178>
Created a new atom named: HN within residue: .R<VAL 179>
Created a new atom named: OXT within residue: .R<VAL 179>
Created a new atom named: HT1 within residue: .R<PHE 180>
Created a new atom named: HT2 within residue: .R<PHE 180>
Created a new atom named: HT3 within residue: .R<PHE 180>
Created a new atom named: HN within residue: .R<CALA 181>
total atoms in file: 2291
Leap added 1141 missing atoms according to residue templates:
1141 H / lone pairs
The file contained 168 atoms not in residue templates
While i input the raw protein file its showing "adding missing heavy
atoms". What is the difference between these?? can anyone explain??
--
With kind regards,
Sreemol
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Received on Wed Mar 09 2016 - 20:30:03 PST
