Dear amber specialists,
When I am simulating the interaction betweem drug and protein containing heme, the parameter of heme was not identified.
Amber has generated the drug.lib and drug.frcmod, heme_all.in and frcmod.hemall are downloaded. All the four files have been loaded in tleap successfully. But the protein complex could not be saved
as follows:
> saveamberparm RRR complex-solvated.prmtop complex-solvated.inpcrd
Checking Unit.
WARNING: There is a bond of 4.977567 angstroms between:
------- .R<R 494>.A<C11 19> and .R<R 494>.A<C13 21>
WARNING: There is a bond of 5.471636 angstroms between:
------- .R<R 494>.A<C4 12> and .R<R 494>.A<C6 14>
WARNING: There is a bond of 3.329748 angstroms between:
------- .R<R 494>.A<N 5> and .R<R 494>.A<C3 11>
WARNING: There is a bond of 7.987354 angstroms between:
------- .R<R 494>.A<S 1> and .R<R 494>.A<C 8>
FATAL: Atom .R<HEM 493>.A<CHA 1> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHB 2> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHC 3> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHD 4> does not have a type.
FATAL: Atom .R<HEM 493>.A<C1A 5> does not have a type.
FATAL: Atom .R<HEM 493>.A<C2A 6> does not have a type.
FATAL: Atom .R<HEM 493>.A<C3A 7> does not have a type.
FATAL: Atom .R<HEM 493>.A<C4A 8> does not have a type.
FATAL: Atom .R<HEM 493>.A<CMA 9> does not have a type.
FATAL: Atom .R<HEM 493>.A<CAA 10> does not have a type.
FATAL: Atom .R<HEM 493>.A<CBA 11> does not have a type.
FATAL: Atom .R<HEM 493>.A<CGA 12> does not have a type.
FATAL: Atom .R<HEM 493>.A<O1A 13> does not have a type.
FATAL: Atom .R<HEM 493>.A<O2A 14> does not have a type.
FATAL: Atom .R<HEM 493>.A<C1B 15> does not have a type.
FATAL: Atom .R<HEM 493>.A<C2B 16> does not have a type.
FATAL: Atom .R<HEM 493>.A<C3B 17> does not have a type.
FATAL: Atom .R<HEM 493>.A<C4B 18> does not have a type.
FATAL: Atom .R<HEM 493>.A<CMB 19> does not have a type.
FATAL: Atom .R<HEM 493>.A<CAB 20> does not have a type.
FATAL: Atom .R<HEM 493>.A<CBB 21> does not have a type.
FATAL: Atom .R<HEM 493>.A<C1C 22> does not have a type.
FATAL: Atom .R<HEM 493>.A<C2C 23> does not have a type.
FATAL: Atom .R<HEM 493>.A<C3C 24> does not have a type.
FATAL: Atom .R<HEM 493>.A<C4C 25> does not have a type.
FATAL: Atom .R<HEM 493>.A<CMC 26> does not have a type.
FATAL: Atom .R<HEM 493>.A<CAC 27> does not have a type.
FATAL: Atom .R<HEM 493>.A<CBC 28> does not have a type.
FATAL: Atom .R<HEM 493>.A<C1D 29> does not have a type.
FATAL: Atom .R<HEM 493>.A<C2D 30> does not have a type.
FATAL: Atom .R<HEM 493>.A<C3D 31> does not have a type.
FATAL: Atom .R<HEM 493>.A<C4D 32> does not have a type.
FATAL: Atom .R<HEM 493>.A<CMD 33> does not have a type.
FATAL: Atom .R<HEM 493>.A<CAD 34> does not have a type.
FATAL: Atom .R<HEM 493>.A<CBD 35> does not have a type.
FATAL: Atom .R<HEM 493>.A<CGD 36> does not have a type.
FATAL: Atom .R<HEM 493>.A<O1D 37> does not have a type.
FATAL: Atom .R<HEM 493>.A<O2D 38> does not have a type.
FATAL: Atom .R<HEM 493>.A<NA 39> does not have a type.
FATAL: Atom .R<HEM 493>.A<NB 40> does not have a type.
FATAL: Atom .R<HEM 493>.A<NC 41> does not have a type.
FATAL: Atom .R<HEM 493>.A<ND 42> does not have a type.
FATAL: Atom .R<HEM 493>.A<FE 43> does not have a type.
My parameter files are also attached.
tianchuan56
tianchuan1015
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- application/octet-stream attachment: R.frcmod
Received on Fri Feb 22 2013 - 00:30:02 PST
