You have atom names in your pdb file that don't match the template. This
is a common question - search on 'Created a new atom named: ' and you'll
probably find a detailed answer. Or 'desc NGLY' in leap to see the
expected names.
Bill
On 3/9/16 8:25 PM, Sreemol G wrote:
> 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??
>
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Received on Wed Mar 09 2016 - 22:00:04 PST
