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From: Jason Swails <jason.swails.gmail.com>

Date: Mon, 22 Mar 2010 18:16:01 -0400

2010/3/22 SimonKao <h88252.hotmail.com>:

*> 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,
*

If it's not in any of the libraries, then you'll need to create an

amber prep (or mol2) file that contains each atom name and its type as

well as its charge. You will then also have to create a frcmod file

that has all force field parameters for the heme that are missing from

the force field.

This process is well-documented in the archives, the tutorials, and the manual.

Good luck!

Jason

*>
*

*> 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
*

*>
*

Date: Mon, 22 Mar 2010 18:16:01 -0400

2010/3/22 SimonKao <h88252.hotmail.com>:

If it's not in any of the libraries, then you'll need to create an

amber prep (or mol2) file that contains each atom name and its type as

well as its charge. You will then also have to create a frcmod file

that has all force field parameters for the heme that are missing from

the force field.

This process is well-documented in the archives, the tutorials, and the manual.

Good luck!

Jason

-- --------------------------------------- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Mar 22 2010 - 15:30:02 PDT

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