AMBER Archive (2007)

Subject: Re: AMBER: heme forcefield atom types

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Sep 11 2007 - 10:05:46 CDT

You need to define all the atom types in the leaprc file under
addAtomTypes { .....

vlad

john chen wrote:

> 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.hemall and 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.
>
>
>
>
>
>
> 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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