Actually i have tried but i'm getting errors when i try to save my topology
and coordinate files.I have used the forcefield "leaprc.ff14SB" when i
loaded pdb i got the message and when i tried to save the topology file and
coordinate file i'm getting following error
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
> saveamberparm com com.prmtop com.inpcrd
Checking Unit.
WARNING: There is a bond of 7.785425 angstroms between:
------- .R<LYS 171>.A<C 21> and .R<GLY 172>.A<N 1>
WARNING: There is a bond of 3.116405 angstroms between:
------- .R<VAL 179>.A<C 15> and .R<PHE 180>.A<N 1>
WARNING: The unperturbed charge of the unit: -17.000000 is not zero.
FATAL: Atom .R<NGLY 18>.A<HT1 10> does not have a type.
FATAL: Atom .R<NGLY 18>.A<HT2 11> does not have a type.
FATAL: Atom .R<NGLY 18>.A<HT3 12> does not have a type.
FATAL: Atom .R<ARG 19>.A<HN 25> does not have a type.
FATAL: Atom .R<THR 20>.A<HN 15> does not have a type.
FATAL: Atom .R<ASN 21>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 22>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 23>.A<HN 20> does not have a type.
FATAL: Atom .R<VAL 24>.A<HN 17> does not have a type.
FATAL: Atom .R<ASN 25>.A<HN 15> does not have a type.
FATAL: Atom .R<TYR 26>.A<HN 22> does not have a type.
FATAL: Atom .R<LEU 27>.A<HN 20> does not have a type.
FATAL: Atom .R<GLN 29>.A<HN 18> does not have a type.
FATAL: Atom .R<ASN 30>.A<HN 15> does not have a type.
FATAL: Atom .R<MET 31>.A<HN 18> does not have a type.
FATAL: Atom .R<THR 32>.A<HN 15> does not have a type.
FATAL: Atom .R<GLN 33>.A<HN 18> does not have a type.
FATAL: Atom .R<ASP 34>.A<HN 13> does not have a type.
FATAL: Atom .R<GLU 35>.A<HN 16> does not have a type.
FATAL: Atom .R<LEU 36>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 37>.A<HN 25> does not have a type.
FATAL: Atom .R<SER 38>.A<HN 12> does not have a type.
FATAL: Atom .R<LEU 39>.A<HN 20> does not have a type.
FATAL: Atom .R<PHE 40>.A<HN 21> does not have a type.
FATAL: Atom .R<SER 41>.A<HN 12> does not have a type.
FATAL: Atom .R<SER 42>.A<HN 12> does not have a type.
FATAL: Atom .R<ILE 43>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 44>.A<HN 8> does not have a type.
FATAL: Atom .R<GLU 45>.A<HN 16> does not have a type.
FATAL: Atom .R<VAL 46>.A<HN 17> does not have a type.
FATAL: Atom .R<GLU 47>.A<HN 16> does not have a type.
FATAL: Atom .R<SER 48>.A<HN 12> does not have a type.
FATAL: Atom .R<ALA 49>.A<HN 11> does not have a type.
FATAL: Atom .R<LYS 50>.A<HN 23> does not have a type.
FATAL: Atom .R<LEU 51>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 52>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 53>.A<HN 25> does not have a type.
FATAL: Atom .R<ASP 54>.A<HN 13> does not have a type.
FATAL: Atom .R<LYS 55>.A<HN 23> does not have a type.
FATAL: Atom .R<VAL 56>.A<HN 17> does not have a type.
FATAL: Atom .R<ALA 57>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 58>.A<HN 8> does not have a type.
FATAL: Atom .R<HIE 59>.A<HN 18> does not have a type.
FATAL: Atom .R<SER 60>.A<HN 12> does not have a type.
FATAL: Atom .R<LEU 61>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 62>.A<HN 8> does not have a type.
FATAL: Atom .R<TYR 63>.A<HN 22> does not have a type.
FATAL: Atom .R<GLY 64>.A<HN 8> does not have a type.
FATAL: Atom .R<PHE 65>.A<HN 21> does not have a type.
FATAL: Atom .R<VAL 66>.A<HN 17> does not have a type.
FATAL: Atom .R<ASN 67>.A<HN 15> does not have a type.
FATAL: Atom .R<TYR 68>.A<HN 22> does not have a type.
FATAL: Atom .R<VAL 69>.A<HN 17> does not have a type.
FATAL: Atom .R<THR 70>.A<HN 15> does not have a type.
FATAL: Atom .R<ALA 71>.A<HN 11> does not have a type.
FATAL: Atom .R<LYS 72>.A<HN 23> does not have a type.
FATAL: Atom .R<ASP 73>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 74>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 75>.A<HN 16> does not have a type.
FATAL: Atom .R<ARG 76>.A<HN 25> does not have a type.
FATAL: Atom .R<ALA 77>.A<HN 11> does not have a type.
FATAL: Atom .R<ILE 78>.A<HN 20> does not have a type.
FATAL: Atom .R<ASN 79>.A<HN 15> does not have a type.
FATAL: Atom .R<THR 80>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 81>.A<HN 20> does not have a type.
FATAL: Atom .R<ASN 82>.A<HN 15> does not have a type.
FATAL: Atom .R<GLY 83>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 84>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 85>.A<HN 25> does not have a type.
FATAL: Atom .R<LEU 86>.A<HN 20> does not have a type.
FATAL: Atom .R<GLN 87>.A<HN 18> does not have a type.
FATAL: Atom .R<SER 88>.A<HN 12> does not have a type.
FATAL: Atom .R<LYS 89>.A<HN 23> does not have a type.
FATAL: Atom .R<THR 90>.A<HN 15> does not have a type.
FATAL: Atom .R<ILE 91>.A<HN 20> does not have a type.
FATAL: Atom .R<LYS 92>.A<HN 23> does not have a type.
FATAL: Atom .R<VAL 93>.A<HN 17> does not have a type.
FATAL: Atom .R<SER 94>.A<HN 12> does not have a type.
FATAL: Atom .R<TYR 95>.A<HN 22> does not have a type.
FATAL: Atom .R<ALA 96>.A<HN 11> does not have a type.
FATAL: Atom .R<ARG 97>.A<HN 25> does not have a type.
FATAL: Atom .R<SER 99>.A<HN 12> does not have a type.
FATAL: Atom .R<SER 100>.A<HN 12> does not have a type.
FATAL: Atom .R<GLU 101>.A<HN 16> does not have a type.
FATAL: Atom .R<VAL 102>.A<HN 17> does not have a type.
FATAL: Atom .R<ILE 103>.A<HN 20> does not have a type.
FATAL: Atom .R<LYS 104>.A<HN 23> does not have a type.
FATAL: Atom .R<ASP 105>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 106>.A<HN 11> does not have a type.
FATAL: Atom .R<ASN 107>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 108>.A<HN 20> does not have a type.
FATAL: Atom .R<TYR 109>.A<HN 22> does not have a type.
FATAL: Atom .R<ILE 110>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 111>.A<HN 12> does not have a type.
FATAL: Atom .R<GLY 112>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 113>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 115>.A<HN 25> does not have a type.
FATAL: Atom .R<THR 116>.A<HN 15> does not have a type.
FATAL: Atom .R<MET 117>.A<HN 18> does not have a type.
FATAL: Atom .R<THR 118>.A<HN 15> does not have a type.
FATAL: Atom .R<GLN 119>.A<HN 18> does not have a type.
FATAL: Atom .R<LYS 120>.A<HN 23> does not have a type.
FATAL: Atom .R<ASP 121>.A<HN 13> does not have a type.
FATAL: Atom .R<VAL 122>.A<HN 17> does not have a type.
FATAL: Atom .R<GLU 123>.A<HN 16> does not have a type.
FATAL: Atom .R<ASP 124>.A<HN 13> does not have a type.
FATAL: Atom .R<MET 125>.A<HN 18> does not have a type.
FATAL: Atom .R<PHE 126>.A<HN 21> does not have a type.
FATAL: Atom .R<SER 127>.A<HN 12> does not have a type.
FATAL: Atom .R<ARG 128>.A<HN 25> does not have a type.
FATAL: Atom .R<PHE 129>.A<HN 21> does not have a type.
FATAL: Atom .R<GLY 130>.A<HN 8> does not have a type.
FATAL: Atom .R<ARG 131>.A<HN 25> does not have a type.
FATAL: Atom .R<ILE 132>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 133>.A<HN 20> does not have a type.
FATAL: Atom .R<ASN 134>.A<HN 15> does not have a type.
FATAL: Atom .R<SER 135>.A<HN 12> does not have a type.
FATAL: Atom .R<ARG 136>.A<HN 25> does not have a type.
FATAL: Atom .R<VAL 137>.A<HN 17> does not have a type.
FATAL: Atom .R<LEU 138>.A<HN 20> does not have a type.
FATAL: Atom .R<VAL 139>.A<HN 17> does not have a type.
FATAL: Atom .R<ASP 140>.A<HN 13> does not have a type.
FATAL: Atom .R<GLN 141>.A<HN 18> does not have a type.
FATAL: Atom .R<THR 142>.A<HN 15> does not have a type.
FATAL: Atom .R<THR 143>.A<HN 15> does not have a type.
FATAL: Atom .R<GLY 144>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 145>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 146>.A<HN 12> does not have a type.
FATAL: Atom .R<ARG 147>.A<HN 25> does not have a type.
FATAL: Atom .R<GLY 148>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 149>.A<HN 17> does not have a type.
FATAL: Atom .R<ALA 150>.A<HN 11> does not have a type.
FATAL: Atom .R<PHE 151>.A<HN 21> does not have a type.
FATAL: Atom .R<ILE 152>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 153>.A<HN 25> does not have a type.
FATAL: Atom .R<PHE 154>.A<HN 21> does not have a type.
FATAL: Atom .R<ASP 155>.A<HN 13> does not have a type.
FATAL: Atom .R<LYS 156>.A<HN 23> does not have a type.
FATAL: Atom .R<ARG 157>.A<HN 25> does not have a type.
FATAL: Atom .R<SER 158>.A<HN 12> does not have a type.
FATAL: Atom .R<GLU 159>.A<HN 16> does not have a type.
FATAL: Atom .R<ALA 160>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 161>.A<HN 16> does not have a type.
FATAL: Atom .R<GLU 162>.A<HN 16> does not have a type.
FATAL: Atom .R<ALA 163>.A<HN 11> does not have a type.
FATAL: Atom .R<ILE 164>.A<HN 20> does not have a type.
FATAL: Atom .R<THR 165>.A<HN 15> does not have a type.
FATAL: Atom .R<SER 166>.A<HN 12> does not have a type.
FATAL: Atom .R<PHE 167>.A<HN 21> does not have a type.
FATAL: Atom .R<ASN 168>.A<HN 15> does not have a type.
FATAL: Atom .R<GLY 169>.A<HN 8> does not have a type.
FATAL: Atom .R<HIE 170>.A<HN 18> does not have a type.
FATAL: Atom .R<LYS 171>.A<HN 23> does not have a type.
FATAL: Atom .R<LYS 171>.A<OXT 24> does not have a type.
FATAL: Atom .R<GLY 172>.A<HT1 8> does not have a type.
FATAL: Atom .R<GLY 172>.A<HT2 9> does not have a type.
FATAL: Atom .R<GLY 172>.A<HT3 10> does not have a type.
FATAL: Atom .R<SER 173>.A<HN 12> does not have a type.
FATAL: Atom .R<SER 174>.A<HN 12> does not have a type.
FATAL: Atom .R<GLU 175>.A<HN 16> does not have a type.
FATAL: Atom .R<ILE 177>.A<HN 20> does not have a type.
FATAL: Atom .R<THR 178>.A<HN 15> does not have a type.
FATAL: Atom .R<VAL 179>.A<HN 17> does not have a type.
FATAL: Atom .R<VAL 179>.A<OXT 18> does not have a type.
FATAL: Atom .R<PHE 180>.A<HT1 21> does not have a type.
FATAL: Atom .R<PHE 180>.A<HT2 22> does not have a type.
FATAL: Atom .R<PHE 180>.A<HT3 23> does not have a type.
FATAL: Atom .R<CALA 181>.A<HN 12> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Can you tell me what may be the reason
On Fri, Mar 11, 2016 at 6:05 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Mar 11, 2016, Sreemol G wrote:
>
> > Can anyone tell me where can i find protein-RNA complex simulation
> > tutorial?? I could able to run simulation for protein and RNA separately
> > with the help of tutorial. But i didnt find tutorial for protein- RNA
> > complex. If anyone knows could you please send it to me??
>
> Running an RNA-protein complex is no different operationally than for RNA
> or
> protein alone. Don't be afraid to try some experiments, and see what you
> get.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 05:00:09 PST
