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From: SimonKao <h88252.hotmail.com>

Date: Tue, 23 Mar 2010 00:05:40 +0800

Dear Amber users,

I tried to make topology file and coordinate file of human oxy-hemoglobin,

but there are some errors happened in Leap.

I use PDB ID:2dn1 as my initial protein structure, ff03 as my force field.

Unfortunately, it does not seem to recognize heme, so I check ff03 in Leap library,

but I do not find any infomation about "heme", I also review some mails in Amber mailing list archive, but I still cannot find any solutions.

And here is one part of my leap.log.

Checking Unit.

WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

FATAL: Atom .R<HEM 289>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 289>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 289>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 289>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 289>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 289>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 289>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 289>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 290>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 290>.A<O2 2> does not have a type.

FATAL: Atom .R<HEM 431>.A<FE 1> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHA 2> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHB 3> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHC 4> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHD 5> does not have a type.

FATAL: Atom .R<HEM 431>.A<NA 6> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1A 7> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2A 8> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3A 9> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4A 10> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMA 11> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAA 12> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBA 13> does not have a type.

FATAL: Atom .R<HEM 431>.A<CGA 14> does not have a type.

FATAL: Atom .R<HEM 431>.A<O1A 15> does not have a type.

FATAL: Atom .R<HEM 431>.A<O2A 16> does not have a type.

FATAL: Atom .R<HEM 431>.A<NB 17> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 431>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 431>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 431>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 431>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 431>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 432>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 432>.A<O2 2> does not have a type.

FATAL: Atom .R<HEM 578>.A<FE 1> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHA 2> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHB 3> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHC 4> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHD 5> does not have a type.

FATAL: Atom .R<HEM 578>.A<NA 6> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1A 7> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2A 8> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3A 9> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4A 10> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMA 11> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAA 12> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBA 13> does not have a type.

FATAL: Atom .R<HEM 578>.A<CGA 14> does not have a type.

FATAL: Atom .R<HEM 578>.A<O1A 15> does not have a type.

FATAL: Atom .R<HEM 578>.A<O2A 16> does not have a type.

FATAL: Atom .R<HEM 578>.A<NB 17> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 578>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 578>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 578>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 578>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 578>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 579>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 579>.A<O2 2> does not have a type.

Failed to generate parameters

Parameter file was not saved.

I shall be very thankful for any suggestion or comments in this regard.

Best regards

----- end ---------------------------------------------------------------------------------

Kao

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 22 2010 - 09:30:03 PDT

Date: Tue, 23 Mar 2010 00:05:40 +0800

Dear Amber users,

I tried to make topology file and coordinate file of human oxy-hemoglobin,

but there are some errors happened in Leap.

I use PDB ID:2dn1 as my initial protein structure, ff03 as my force field.

Unfortunately, it does not seem to recognize heme, so I check ff03 in Leap library,

but I do not find any infomation about "heme", I also review some mails in Amber mailing list archive, but I still cannot find any solutions.

And here is one part of my leap.log.

Checking Unit.

WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

FATAL: Atom .R<HEM 289>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 289>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 289>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 289>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 289>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 289>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 289>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 289>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 289>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 289>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 289>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 289>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 289>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 289>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 290>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 290>.A<O2 2> does not have a type.

FATAL: Atom .R<HEM 431>.A<FE 1> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHA 2> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHB 3> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHC 4> does not have a type.

FATAL: Atom .R<HEM 431>.A<CHD 5> does not have a type.

FATAL: Atom .R<HEM 431>.A<NA 6> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1A 7> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2A 8> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3A 9> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4A 10> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMA 11> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAA 12> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBA 13> does not have a type.

FATAL: Atom .R<HEM 431>.A<CGA 14> does not have a type.

FATAL: Atom .R<HEM 431>.A<O1A 15> does not have a type.

FATAL: Atom .R<HEM 431>.A<O2A 16> does not have a type.

FATAL: Atom .R<HEM 431>.A<NB 17> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 431>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 431>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 431>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 431>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 431>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 431>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 431>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 431>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 431>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 431>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 431>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 431>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 432>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 432>.A<O2 2> does not have a type.

FATAL: Atom .R<HEM 578>.A<FE 1> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHA 2> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHB 3> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHC 4> does not have a type.

FATAL: Atom .R<HEM 578>.A<CHD 5> does not have a type.

FATAL: Atom .R<HEM 578>.A<NA 6> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1A 7> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2A 8> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3A 9> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4A 10> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMA 11> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAA 12> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBA 13> does not have a type.

FATAL: Atom .R<HEM 578>.A<CGA 14> does not have a type.

FATAL: Atom .R<HEM 578>.A<O1A 15> does not have a type.

FATAL: Atom .R<HEM 578>.A<O2A 16> does not have a type.

FATAL: Atom .R<HEM 578>.A<NB 17> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1B 18> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2B 19> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3B 20> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4B 21> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMB 22> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAB 23> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBB 24> does not have a type.

FATAL: Atom .R<HEM 578>.A<NC 25> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1C 26> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2C 27> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3C 28> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4C 29> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMC 30> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAC 31> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBC 32> does not have a type.

FATAL: Atom .R<HEM 578>.A<ND 33> does not have a type.

FATAL: Atom .R<HEM 578>.A<C1D 34> does not have a type.

FATAL: Atom .R<HEM 578>.A<C2D 35> does not have a type.

FATAL: Atom .R<HEM 578>.A<C3D 36> does not have a type.

FATAL: Atom .R<HEM 578>.A<C4D 37> does not have a type.

FATAL: Atom .R<HEM 578>.A<CMD 38> does not have a type.

FATAL: Atom .R<HEM 578>.A<CAD 39> does not have a type.

FATAL: Atom .R<HEM 578>.A<CBD 40> does not have a type.

FATAL: Atom .R<HEM 578>.A<CGD 41> does not have a type.

FATAL: Atom .R<HEM 578>.A<O1D 42> does not have a type.

FATAL: Atom .R<HEM 578>.A<O2D 43> does not have a type.

FATAL: Atom .R<O2 579>.A<O1 1> does not have a type.

FATAL: Atom .R<O2 579>.A<O2 2> does not have a type.

Failed to generate parameters

Parameter file was not saved.

I shall be very thankful for any suggestion or comments in this regard.

Best regards

----- end ---------------------------------------------------------------------------------

Kao

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 22 2010 - 09:30:03 PDT

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