Prajwal Nandekar <prajwal.pharm07.gmail.com> wrote:
> Dear tianchuan1015,
>
> Yes, It seems the heme_all.frcmod is successfully load into leap.
> Dont worry, ignore these errors and proceed for next steps.
I question that advice. It seems the file is garbled, so who knows
what the validity of the downstream result would be.
Bill
> For heme you dont need to do any changes in protein and heme.
> these files are working fine (I already tried these files for your complex
> here)
> Only thing is to re-prepare ligand parameters (frcmod) file.
> So, No need to modify anything in your protein and heme.
> These are parameters for heme with Cys bound state. (same is the case in
> your CYP).
>
> All the best
>
> On Fri, Feb 22, 2013 at 8:01 PM, tianchuan1015 <tianchuan1015.gmail.com>wrote:
>
> > **
> > Dear Prajwal Nandekar <prajwal.pharm07.gmail.com>,
> > I really appreciate for your help! I used the files you offered. But
> > when I load heme_all.frcmod, there comes errors as follows:
> >
> > > loadamberparams heme_all.frcmod
> > Loading parameters: ./heme_all.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Force field modifications for all-atom heme
> > Unknown keyword:
> > in parameter file.
> > Unknown keyword: NP in parameter file.
> > Unknown keyword:
> > in parameter file.
> > Unknown keyword: CX in parameter file.
> > Unknown keyword:
> > in parameter file.
> >
> > Besides, the heme forms disulfide linkage with residue cys. I
> > have changed CYS to CYX. Is this enough or what else should I modify.
> >
> > sincerely,
> > tianchuan
> > ------------------------------
> > tianchuan1015
> >
> > *From:* Prajwal Nandekar <prajwal.pharm07.gmail.com>
> > *Date:* 2013-02-22 18:12
> > *To:* tianchuan1015 <tianchuan1015.gmail.com>; AMBER Mailing List<amber.ambermd.org>
> > *Subject:* Re: [AMBER] amber error about protein containing heme
> > Dear tianchuan56,
> >
> > I think you are CYP450 system with heme and ligand.
> > The problem is in the "frcmod.hemeall" and "heme_all.in" files. These
> > files doesn't have proper parameters for heme.
> > I have validated prepin and frcmod files of heme [attached in mail
> > filename (1) heme_all.prepin and (2) heme_all.frcmod].
> > Please use those files for system preparation.
> >
> > commands in tleap or xleap:
> > loadamberprep heme_all.prepin
> > loadamberparams heme_all.frcmod
> >
> > One more thing I observed in frcmod file of ligand (R.frcmod) is also not
> > properly defined bond angle and atom types.
> > Please re-prepare it.
> >
> > In your CYP-ligand complex, The distance between some atoms of ligand R is
> > in close proximity to some atoms of heme. (I.e. these are in bonding
> > distance) This condition should not be happen in case of CYP450s.
> > Please pay attention towards these issues.
> >
> > All the best
> >
> >
> > On Fri, Feb 22, 2013 at 1:28 PM, tianchuan1015 <tianchuan1015.gmail.com>wrote:
> >
> >> 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > *Thanks and Regards,
> >
> > ---------------------------------------------
> > Prajwal Nandekar
> > Ph. D. Scholar
> > Department of Pharmacoinformatics
> > National Institute of Pharmaceutical Education and Research (NIPER)
> > Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
> > Mob. 09780741228*
> >
>
>
>
> --
> *Thanks and Regards,
>
> ---------------------------------------------
> Prajwal Nandekar
> Ph. D. Scholar
> Department of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
> Mob. 09780741228*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 23 2013 - 12:30:02 PST
