On Mon, 2014-03-17 at 15:43 +0900, Rajiv Gandhi wrote:
> Hello,
>
> I have been trying to do MD simulation on myoglobin in AMBER.
>
> To do so, I used the parameter file of updated Gilmma heme parameter (
> http://archive.ambermd.org/201012/att-0192/) and couldn't get success to
> create the parameter files from them.
>
> Could you please let me know how i can deal the protein with heme-co ???
>
> I just tried with myoglobin contains heme+co and got error on reading it...
>
> Its really appreciated if you could give some hints on this. Thanks a lot
> for your time. Have a good day
First piece of advice: give your emails a subject. I suspect your first
email was caught by my spam filter for precisely that reason. Useful
subject headings also lets people filter which emails to respond based
on their expertise quickly. Many people skip emails with no subject for
that reason.
My responses to your questions are below:
> > > loadamberparams frcmod.hemall
> > Loading parameters: ./frcmod.hemall
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Force field modifcations for all-atom heme
> > Unknown keyword:
> > in parameter file. Perhaps a format error?
> > Unknown keyword:
> > in parameter file. Perhaps a format error?
> > Unknown keyword:
> > in parameter file. Perhaps a format error?
> > Unknown keyword:
> > in parameter file. Perhaps a format error?
I believe this error is due to the fact that the frcmod.hemall file you
downloaded has dos line endings. I get the same warnings/error messages
here that you get when I download the file and load it in tleap. If I
run the file through the dos2unix program (which converts DOS-style line
endings to UNIX-style newlines), these error messages go away.
To be safe, you should probably run heme_all.in through dos2unix as
well.
> > FATAL: Atom .R<CMO 155>.A<LO 2> does not have a type.
> > FATAL: Atom .R<CMO 155>.A<LC 1> does not have a type.
Have you defined the CMO residue anywhere? If you use the "list"
command in tleap, it should show "CMO" somewhere. I suspect you have
not created a library file (mol2, prep, or Amber OFF) for CMO, so tleap
does not know what atom types to assign to LO and LC.
> > Warning: Close contact of 1.139998 angstroms between .R<HIP 24>.A<HE2 14>
> > and .R<HIP 119>.A<HE2 14>
> > Warning: Close contact of 0.994947 angstroms between .R<HIP 93>.A<HE2 14>
> > and .R<HEM 154>.A<FE 1>
> > Checking parameters for unit 'X'.
> > Checking for bond parameters.
> > Could not find bond parameter for: -
> > Checking for angle parameters.
> > There are missing parameters.
> > check: Errors: 2 Warnings: 3
> >
> >
> > *After mentioning the bond, i get more error as follows: *
> >
> > > bond X.93.NE2 X.154.FE
> > > bond X.154.FE X.155.LC <http://x.155.lc/>
> > > check X
> > Checking 'X'....
> > WARNING: The unperturbed charge of the unit: 12.000000 is not zero.
> > FATAL: Atom .R<CMO 155>.A<LO 2> does not have a type.
> > FATAL: Atom .R<CMO 155>.A<LC 1> does not have a type.
> > Warning: Close contact of 1.139998 angstroms between .R<HIP 24>.A<HE2 14>
> > and .R<HIP 119>.A<HE2 14>
> > Warning: Close contact of 0.994947 angstroms between .R<HIP 93>.A<HE2 14>
> > and .R<HEM 154>.A<FE 1>
> > Checking parameters for unit 'X'.
> > Checking for bond parameters.
> > Could not find bond parameter for: NA - FE
> > Could not find bond parameter for: FE -
> > Could not find bond parameter for: -
> > Checking for angle parameters.
> > Could not find angle parameter: CW - NA - FE
> > Could not find angle parameter: H - NA - FE
> > Could not find angle parameter: NA - FE - NP
> > Could not find angle parameter: NA - FE - NO
> > Could not find angle parameter: NA - FE - NP
> > Could not find angle parameter: NA - FE - NO
> > Could not find angle parameter: NA - FE -
> > Could not find angle parameter: CR - NA - FE
> > Could not find angle parameter: NO - FE -
> > Could not find angle parameter: NP - FE -
> > Could not find angle parameter: NO - FE -
> > Could not find angle parameter: NP - FE -
> > Could not find angle parameter: FE - -
You will need to find parameters for all of these terms if you add bonds
by hand in tleap. You have to define these parameters in an frcmod file
and then load those in your tleap script.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 17 2014 - 05:30:02 PDT
