AMBER Archive (2007)

Subject: AMBER: heme forcefield atom types

From: john chen (johnchen51_at_gmail.com)
Date: Tue Sep 11 2007 - 09:09:45 CDT

Dear amber-experts,

I am trying to make topology and coordinate files for a protein with a heme
using tleap.
I am using amber 9. I want to use the ff99SB force-field and the parameter
files for heme
(heme_all.in and frcmod.hemall) which are in
../mydirectory/dat/contrib/heme.

>From the X-ray structure, I first run the subroutine protonate. The protons
are added with no
difficulties. Then in tleap, I run the scrip below.. everything seems to run
fine: the frcmod and prepin
files for the heme are read in, and even on the command 'check' there seems
to be no problems.
However, the program cannot find certain atom types for the heme.

I applogise for my ignorance, but is this information not in
frcmod.hemalland heme_all.in ?

I would appreciate it if somebody could tell me what I have done wrong. Is
there another
file that I have to define?

with best regards,

JC.

>source leaprc.ff99SB

>loadamberparams /mydirectory/dat/contrib/heme/frcmod.hemall

Loading parameters: /mydirectory/dat/contrib/heme/frcmod.hemall
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme
Unknown keyword: N.B.: para in parameter file.
Unknown keyword: six-coo in parameter file.
Unknown keyword: Force fiel in parameter file.
Unknown keyword: Univers in parameter file.
Unknown keyword: in parameter file.
Unknown keyword: I modified in parameter file.

>loadamberprep /mydirectory/dat/contrib/heme/heme_all.in

Loading Prep file: /mydirectory/dat/contrib/heme/heme_all.in
(no charges read on atoms lines in Heme residue ALL ATOM, Yves names,
Bayly-modified)

>mol = loadpdb mymol.pdb

  Loading PDB file: ./holoH.pdb
  Added missing heavy atom: .R<CALA 88>.A<OXT 11>
  total atoms in file: 1270
  Leap added 1 missing atom according to residue templates:
       1 Heavy

>check mol

Checking 'mol'....
WARNING: The unperturbed charge of the unit: -8.000000 is not zero.
Checking parameters for unit 'temp'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.

>saveamberparm mol mol.top mol.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -8.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
For atom: .R<HEM 89>.A<NA 2> Could not find type: NP
For atom: .R<HEM 89>.A<NB 23> Could not find type: NO
For atom: .R<HEM 89>.A<CBB 32> Could not find type: CX
For atom: .R<HEM 89>.A<NC 39> Could not find type: NP
For atom: .R<HEM 89>.A<CBC 48> Could not find type: CX
For atom: .R<HEM 89>.A<ND 55> Could not find type: NO
Parameter file was not saved.

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