Dear Amber developers:
Some trouble bothered me when I simulated my protein and ligand with amber following amber tutorial 'Using Antechamber to Create LEaP Input Files for Simulating Sustiva (efavirenz)-RT complex
using the General Amber Force Field' .I successfully created ligand's lib file,inprcd file and prmtop file.Then I tried to created complex's inprcd and prmtop file.
tleap -f oldff/leaprc.ff99SB
source leaprc.gaff
loadamberparams DBP.frcmod
loadoff sus.lib
complex = loadpdb EstJ6_DBP_bound_sus.pdb
These above steps are correct.When I type the following commmand :
saveamberparm complex EstJ6_DBP_bound_sus.prmtop EstJ6_DBP_bound_sus.inpcrd
some problems had arisen:
FATAL: Atom .R<NMET 1>.A<HN1 20> does not have a type.
FATAL: Atom .R<NMET 1>.A<HN2 21> does not have a type.
FATAL: Atom .R<NMET 1>.A<HN3 22> does not have a type.
FATAL: Atom .R<ALA 2>.A<HN 11> does not have a type.
FATAL: Atom .R<SER 3>.A<HN 12> does not have a type.
FATAL: Atom .R<GLN 5>.A<HN 18> does not have a type.
FATAL: Atom .R<LEU 6>.A<HN 20> does not have a type.
FATAL: Atom .R<GLN 7>.A<HN 18> does not have a type.
FATAL: Atom .R<MET 8>.A<HN 18> does not have a type.
FATAL: Atom .R<ALA 9>.A<HN 11> does not have a type.
FATAL: Atom .R<LEU 10>.A<HN 20> does not have a type.
FATAL: Atom .R<ASP 11>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 12>.A<HN 11> does not have a type.
FATAL: Atom .R<PHE 13>.A<HN 21> does not have a type.
FATAL: Atom .R<LYS 14>.A<HN 23> does not have a type.
FATAL: Atom .R<THR 15>.A<HN 15> does not have a type.
FATAL: Atom .R<MET 16>.A<HN 18> does not have a type.
FATAL: Atom .R<GLY 17>.A<HN 8> does not have a type.
FATAL: Atom .R<GLU 18>.A<HN 16> does not have a type.
FATAL: Atom .R<LYS 19>.A<HN 23> does not have a type.
FATAL: Atom .R<MET 20>.A<HN 18> does not have a type.
FATAL: Atom .R<ALA 21>.A<HN 11> does not have a type.
FATAL: Atom .R<GLN 22>.A<HN 18> does not have a type.
FATAL: Atom .R<ALA 23>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 24>.A<HN 8> does not have a type.
FATAL: Atom .R<ASN 25>.A<HN 15> does not have a type.
FATAL: Atom .R<ASP 26>.A<HN 13> does not have a type.
FATAL: Atom .R<VAL 27>.A<HN 17> does not have a type.
FATAL: Atom .R<LYS 28>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 29>.A<HN 11> does not have a type.
FATAL: Atom .R<LEU 30>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 31>.A<HN 25> does not have a type.
FATAL: Atom .R<ALA 32>.A<HN 11> does not have a type.
FATAL: Atom .R<VAL 33>.A<HN 17> does not have a type.
FATAL: Atom .R<MET 34>.A<HN 18> does not have a type.
FATAL: Atom .R<GLU 35>.A<HN 16> does not have a type.
FATAL: Atom .R<GLU 36>.A<HN 16> does not have a type.
FATAL: Atom .R<MET 37>.A<HN 18> does not have a type.
FATAL: Atom .R<SER 38>.A<HN 12> does not have a type.
FATAL: Atom .R<GLY 39>.A<HN 8> does not have a type.
FATAL: Atom .R<PHE 40>.A<HN 21> does not have a type.
FATAL: Atom .R<SER 42>.A<HN 12> does not have a type.
FATAL: Atom .R<ALA 43>.A<HN 11> 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<THR 46>.A<HN 15> does not have a type.
FATAL: Atom .R<LYS 47>.A<HN 23> does not have a type.
FATAL: Atom .R<CYS 48>.A<HN 12> does not have a type.
FATAL: Atom .R<THR 49>.A<HN 15> does not have a type.
FATAL: Atom .R<VAL 51>.A<HN 17> does not have a type.
FATAL: Atom .R<ASN 52>.A<HN 15> does not have a type.
FATAL: Atom .R<ALA 53>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 54>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 55>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 56>.A<HN 17> does not have a type.
FATAL: Atom .R<ALA 58>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 59>.A<HN 16> does not have a type.
FATAL: Atom .R<TRP 60>.A<HN 25> does not have a type.
FATAL: Atom .R<ILE 61>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 62>.A<HN 12> does not have a type.
FATAL: Atom .R<GLY 63>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 65>.A<HN 8> does not have a type.
FATAL: Atom .R<ALA 66>.A<HN 11> does not have a type.
FATAL: Atom .R<ALA 67>.A<HN 11> does not have a type.
FATAL: Atom .R<ASP 68>.A<HN 13> does not have a type.
FATAL: Atom .R<ASP 69>.A<HN 13> does not have a type.
FATAL: Atom .R<ARG 70>.A<HN 25> does not have a type.
FATAL: Atom .R<VAL 71>.A<HN 17> does not have a type.
FATAL: Atom .R<ILE 72>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 73>.A<HN 20> does not have a type.
FATAL: Atom .R<TYR 74>.A<HN 22> does not have a type.
FATAL: Atom .R<VAL 75>.A<HN 17> does not have a type.
FATAL: Atom .R<HIE 76>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 76>.A<HD1 19> does not have a type.
FATAL: Atom .R<GLY 77>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 78>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 79>.A<HN 8> does not have a type.
FATAL: Atom .R<TYR 80>.A<HN 22> does not have a type.
FATAL: Atom .R<VAL 81>.A<HN 17> does not have a type.
FATAL: Atom .R<MET 82>.A<HN 18> does not have a type.
FATAL: Atom .R<GLY 83>.A<HN 8> does not have a type.
FATAL: Atom .R<SER 84>.A<HN 12> does not have a type.
FATAL: Atom .R<ILE 85>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 86>.A<HN 11> does not have a type.
FATAL: Atom .R<THR 87>.A<HN 15> does not have a type.
FATAL: Atom .R<HIE 88>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 88>.A<HD1 19> does not have a type.
FATAL: Atom .R<ARG 89>.A<HN 25> does not have a type.
FATAL: Atom .R<GLU 90>.A<HN 16> does not have a type.
FATAL: Atom .R<THR 91>.A<HN 15> does not have a type.
FATAL: Atom .R<VAL 92>.A<HN 17> does not have a type.
FATAL: Atom .R<ALA 93>.A<HN 11> does not have a type.
FATAL: Atom .R<ARG 94>.A<HN 25> does not have a type.
FATAL: Atom .R<LEU 95>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 96>.A<HN 12> does not have a type.
FATAL: Atom .R<LYS 97>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 98>.A<HN 11> does not have a type.
FATAL: Atom .R<SER 99>.A<HN 12> does not have a type.
FATAL: Atom .R<GLY 100>.A<HN 8> does not have a type.
FATAL: Atom .R<ALA 101>.A<HN 11> does not have a type.
FATAL: Atom .R<ARG 102>.A<HN 25> does not have a type.
FATAL: Atom .R<GLY 103>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 104>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 105>.A<HN 11> does not have a type.
FATAL: Atom .R<LEU 106>.A<HN 20> does not have a type.
FATAL: Atom .R<ASP 107>.A<HN 13> does not have a type.
FATAL: Atom .R<TYR 108>.A<HN 22> does not have a type.
FATAL: Atom .R<ARG 109>.A<HN 25> does not have a type.
FATAL: Atom .R<LEU 110>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 111>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 113>.A<HN 16> does not have a type.
FATAL: Atom .R<HIE 114>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 114>.A<HD1 19> does not have a type.
FATAL: Atom .R<PHE 116>.A<HN 21> does not have a type.
FATAL: Atom .R<ALA 118>.A<HN 11> does not have a type.
FATAL: Atom .R<ALA 119>.A<HN 11> does not have a type.
FATAL: Atom .R<VAL 120>.A<HN 17> does not have a type.
FATAL: Atom .R<ASP 121>.A<HN 13> does not have a type.
FATAL: Atom .R<ASP 122>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 123>.A<HN 11> does not have a type.
FATAL: Atom .R<THR 124>.A<HN 15> does not have a type.
FATAL: Atom .R<ALA 125>.A<HN 11> does not have a type.
FATAL: Atom .R<ALA 126>.A<HN 11> does not have a type.
FATAL: Atom .R<TYR 127>.A<HN 22> does not have a type.
FATAL: Atom .R<ARG 128>.A<HN 25> does not have a type.
FATAL: Atom .R<TRP 129>.A<HN 25> does not have a type.
FATAL: Atom .R<LEU 130>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 131>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 132>.A<HN 12> does not have a type.
FATAL: Atom .R<GLN 133>.A<HN 18> does not have a type.
FATAL: Atom .R<ASN 134>.A<HN 15> does not have a type.
FATAL: Atom .R<ILE 135>.A<HN 20> does not have a type.
FATAL: Atom .R<LYS 136>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 138>.A<HN 11> does not have a type.
FATAL: Atom .R<HIE 139>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 139>.A<HD1 19> does not have a type.
FATAL: Atom .R<ILE 140>.A<HN 20> does not have a type.
FATAL: Atom .R<VAL 141>.A<HN 17> does not have a type.
FATAL: Atom .R<ILE 142>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 143>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 144>.A<HN 8> does not have a type.
FATAL: Atom .R<ASP 145>.A<HN 13> does not have a type.
FATAL: Atom .R<SER 146>.A<HN 12> does not have a type.
FATAL: Atom .R<ALA 147>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 148>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 149>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 150>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 151>.A<HN 20> does not have a type.
FATAL: Atom .R<THR 152>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 153>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 154>.A<HN 11> does not have a type.
FATAL: Atom .R<THR 155>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 156>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 157>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 158>.A<HN 11> does not have a type.
FATAL: Atom .R<LEU 159>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 160>.A<HN 25> does not have a type.
FATAL: Atom .R<ASP 161>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 162>.A<HN 11> does not have a type.
FATAL: Atom .R<LYS 163>.A<HN 23> does not have a type.
FATAL: Atom .R<VAL 164>.A<HN 17> does not have a type.
FATAL: Atom .R<LEU 166>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 168>.A<HN 11> does not have a type.
FATAL: Atom .R<ALA 169>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 170>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 171>.A<HN 17> does not have a type.
FATAL: Atom .R<CYS 172>.A<HN 12> does not have a type.
FATAL: Atom .R<ILE 173>.A<HN 20> does not have a type.
FATAL: Atom .R<SER 174>.A<HN 12> does not have a type.
FATAL: Atom .R<TRP 176>.A<HN 25> does not have a type.
FATAL: Atom .R<THR 177>.A<HN 15> does not have a type.
FATAL: Atom .R<ASP 178>.A<HN 13> does not have a type.
FATAL: Atom .R<MET 179>.A<HN 18> does not have a type.
FATAL: Atom .R<GLU 180>.A<HN 16> does not have a type.
FATAL: Atom .R<GLY 181>.A<HN 8> does not have a type.
FATAL: Atom .R<ALA 182>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 183>.A<HN 8> does not have a type.
FATAL: Atom .R<GLU 184>.A<HN 16> does not have a type.
FATAL: Atom .R<SER 185>.A<HN 12> does not have a type.
FATAL: Atom .R<MET 186>.A<HN 18> does not have a type.
FATAL: Atom .R<THR 187>.A<HN 15> does not have a type.
FATAL: Atom .R<THR 188>.A<HN 15> does not have a type.
FATAL: Atom .R<ARG 189>.A<HN 25> does not have a type.
FATAL: Atom .R<ALA 190>.A<HN 11> does not have a type.
FATAL: Atom .R<LYS 191>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 192>.A<HN 11> does not have a type.
FATAL: Atom .R<ASP 193>.A<HN 13> does not have a type.
FATAL: Atom .R<VAL 195>.A<HN 17> does not have a type.
FATAL: Atom .R<VAL 196>.A<HN 17> does not have a type.
FATAL: Atom .R<GLN 197>.A<HN 18> does not have a type.
FATAL: Atom .R<LYS 198>.A<HN 23> does not have a type.
FATAL: Atom .R<GLN 199>.A<HN 18> does not have a type.
FATAL: Atom .R<GLY 200>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 201>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 202>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 203>.A<HN 8> does not have a type.
FATAL: Atom .R<MET 204>.A<HN 18> does not have a type.
FATAL: Atom .R<ALA 205>.A<HN 11> does not have a type.
FATAL: Atom .R<GLN 206>.A<HN 18> does not have a type.
FATAL: Atom .R<LEU 207>.A<HN 20> does not have a type.
FATAL: Atom .R<TYR 208>.A<HN 22> does not have a type.
FATAL: Atom .R<LEU 209>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 210>.A<HN 8> does not have a type.
FATAL: Atom .R<GLY 211>.A<HN 8> does not have a type.
FATAL: Atom .R<LYS 212>.A<HN 23> does not have a type.
FATAL: Atom .R<ASP 213>.A<HN 13> does not have a type.
FATAL: Atom .R<LYS 215>.A<HN 23> does not have a type.
FATAL: Atom .R<SER 216>.A<HN 12> does not have a type.
FATAL: Atom .R<LEU 218>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 219>.A<HN 11> does not have a type.
FATAL: Atom .R<ALA 220>.A<HN 11> does not have a type.
FATAL: Atom .R<LEU 222>.A<HN 20> does not have a type.
FATAL: Atom .R<HIE 223>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 223>.A<HD1 19> does not have a type.
FATAL: Atom .R<ALA 224>.A<HN 11> does not have a type.
FATAL: Atom .R<ASN 225>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 226>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 227>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 228>.A<HN 8> does not have a type.
FATAL: Atom .R<LEU 229>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 232>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 233>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 234>.A<HN 20> does not have a type.
FATAL: Atom .R<GLN 235>.A<HN 18> does not have a type.
FATAL: Atom .R<VAL 236>.A<HN 17> does not have a type.
FATAL: Atom .R<GLY 237>.A<HN 8> does not have a type.
FATAL: Atom .R<ASP 238>.A<HN 13> does not have a type.
FATAL: Atom .R<ALA 239>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 240>.A<HN 16> does not have a type.
FATAL: Atom .R<THR 241>.A<HN 15> does not have a type.
FATAL: Atom .R<LEU 242>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 243>.A<HN 20> does not have a type.
FATAL: Atom .R<ASP 244>.A<HN 13> does not have a type.
FATAL: Atom .R<ASP 245>.A<HN 13> does not have a type.
FATAL: Atom .R<SER 246>.A<HN 12> does not have a type.
FATAL: Atom .R<ILE 247>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 248>.A<HN 25> does not have a type.
FATAL: Atom .R<VAL 249>.A<HN 17> does not have a type.
FATAL: Atom .R<ALA 250>.A<HN 11> does not have a type.
FATAL: Atom .R<GLU 251>.A<HN 16> does not have a type.
FATAL: Atom .R<LYS 252>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 253>.A<HN 11> does not have a type.
FATAL: Atom .R<LYS 254>.A<HN 23> does not have a type.
FATAL: Atom .R<LYS 255>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 256>.A<HN 11> does not have a type.
FATAL: Atom .R<GLY 257>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 258>.A<HN 17> does not have a type.
FATAL: Atom .R<LYS 259>.A<HN 23> does not have a type.
FATAL: Atom .R<VAL 260>.A<HN 17> does not have a type.
FATAL: Atom .R<ASP 261>.A<HN 13> does not have a type.
FATAL: Atom .R<LEU 262>.A<HN 20> does not have a type.
FATAL: Atom .R<GLU 263>.A<HN 16> does not have a type.
FATAL: Atom .R<VAL 264>.A<HN 17> does not have a type.
FATAL: Atom .R<TRP 265>.A<HN 25> does not have a type.
FATAL: Atom .R<GLU 267>.A<HN 16> does not have a type.
FATAL: Atom .R<MET 268>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 270>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 270>.A<HD1 19> does not have a type.
FATAL: Atom .R<VAL 271>.A<HN 17> does not have a type.
FATAL: Atom .R<TRP 272>.A<HN 25> does not have a type.
FATAL: Atom .R<HIE 273>.A<HN 18> does not have a type.
FATAL: Atom .R<HIE 273>.A<HD1 19> does not have a type.
FATAL: Atom .R<LEU 274>.A<HN 20> does not have a type.
FATAL: Atom .R<PHE 275>.A<HN 21> does not have a type.
FATAL: Atom .R<ALA 276>.A<HN 11> does not have a type.
FATAL: Atom .R<PHE 278>.A<HN 21> does not have a type.
FATAL: Atom .R<LEU 279>.A<HN 20> does not have a type.
FATAL: Atom .R<GLU 281>.A<HN 16> does not have a type.
FATAL: Atom .R<GLY 282>.A<HN 8> does not have a type.
FATAL: Atom .R<GLN 283>.A<HN 18> does not have a type.
FATAL: Atom .R<GLN 284>.A<HN 18> does not have a type.
FATAL: Atom .R<ALA 285>.A<HN 11> does not have a type.
FATAL: Atom .R<ILE 286>.A<HN 20> does not have a type.
FATAL: Atom .R<ASP 287>.A<HN 13> does not have a type.
FATAL: Atom .R<LYS 288>.A<HN 23> does not have a type.
FATAL: Atom .R<ILE 289>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 290>.A<HN 8> does not have a type.
FATAL: Atom .R<LYS 291>.A<HN 23> does not have a type.
FATAL: Atom .R<TYR 292>.A<HN 22> does not have a type.
FATAL: Atom .R<VAL 293>.A<HN 17> does not have a type.
FATAL: Atom .R<ARG 294>.A<HN 25> does not have a type.
FATAL: Atom .R<GLN 295>.A<HN 18> does not have a type.
FATAL: Atom .R<ILE 296>.A<HN 20> does not have a type.
FATAL: Atom .R<THR 297>.A<HN 15> does not have a type.
FATAL: Atom .R<CALA 298>.A<HN 12> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved
Could you give me some suggestions?I'm looking forward to your reply.
Regards
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- application/octet-stream attachment: EstJ6.pdb
- application/octet-stream attachment: DBP.pdb
Received on Thu Sep 19 2019 - 06:00:01 PDT
