Thanks everyone for making thing clear. So I think I am going to manually
change the radii from 2.2A to 1.7A.
Best
NHAI
On Fri, Feb 17, 2012 at 12:06 PM, Ilyas Yildirim <
i-yildirim.northwestern.edu> wrote:
> Nhai -
>
> Niel is right. The atom types of atoms C6 and C8 (pyrimidine and purine)
> in parmCHI_YIL are C3/C4 (Cytidine/Uridine) and C1/C2
> (Adenosine/Guanosine).
>
> [Check $AMBERHOME/dat/leap/parm/frcmod.parmCHI_YIL].
>
> These atom types are the reason why you get radii=2.2 for these carbon
> atoms. In $AMBERHOME/AmberTools/src/leap/src/leap/unitio.c , when mbondi2
> is selected, iGB = 6 (iGBparm = 6). Here is the relevant part from
> unitio.c file:
>
>
> ------------------------------------------------------------------------------
> .
> .
> .
> if( GDefaults.iGBparm < 3 || GDefaults.iGBparm == 6 ) {
> .
> .
> .
> case 6:
> if ( strncmp(sType,"C1",2) && strncmp(sType,"C2",2) && strncmp
> (sType,"C3",2) )
> dGBrad = 1.7;
> else
> dGBrad = 2.2;
> break;
> .
> .
> .
>
> ------------------------------------------------------------------------------
>
> When carbon atoms are checked, it gives a radii=1.7 for those which do not
> have atom types of C1,C2,C3. In amber9, there are no such comparisons done
> for mbondi2. The question is this: Why are the atom types compared? The
> force field that have atom types C1,C2,C3 are
>
> opls_parm.dat
> parm91.dat
> parm91X.dat
> parm91X.ua.dat
> toyrna.dat
>
> and these force fields are defined in amber9, too.
>
> In any case, you can make the necessary changes in the code to let those
> carbon atoms have a radii of 1.7. I think if you play with the above
> lines, that will be enough; but of course it will be wise to know why the
> extra code was written before making the changes. Probably someone in the
> list knows why the extra code was written in unitio.c.
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> On Fri, 17 Feb 2012, Niel Henriksen wrote:
>
> > NHAI,
> >
> > It it likely that leap is not recognizing the atom types
> > used in parmCHI_YIL. You might need to do some
> > hacking around to get it correct.
> >
> > As an additional note, some of the PB code does not
> > recognize some of the newer atom types (like chiOL),
> > at least in amber11. I haven't checked the developer
> > code.
> >
> > --Niel
> > ________________________________________
> > From: Mike NG [nhai.qn.gmail.com]
> > Sent: Friday, February 17, 2012 8:47 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc
> for RNA
> >
> > Hi Jason,
> >
> > It makes no sense to me that changing forcefield from ff10 to
> > leaprc.parmCHI_YIL.bsc could change some C radii. mbondi2 radii was
> > specified in tleap for GB run. I don't think mbondi2 has 2.2 A radius
> for C
> > and this radius value is not allowed to work with igb=7.
> >
> > NHAI
> >
> > On Fri, Feb 17, 2012 at 7:49 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> Some carbon atom types have a radius of 2.2 Angstroms. Have you looked
> at
> >> the code that assigns the atom radii in leap?
> >>
> >> You can look at the code that does this in parmed (changeradii.py) if
> you
> >> have ready access to the developer files. The logic is exactly the same
> (it
> >> was copied out of tleap) and it should be easier to read.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >>
> >> On Feb 16, 2012, at 11:38 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >>> Dear Amber community,
> >>> I want to generate a topology and coordinate file for an RNA structure
> >> with
> >>> parmCHI_YIL.bsc (from Ambertools 1.5, applied bugfix) for GB
> simulation.
> >>> Here is the input file for tleap
> >>>
> >>> source leaprc.parmCHI_YIL.bsc
> >>> set default PBradii mbondi2
> >>> x = loadpdb RNA_ss_UUCG.pdb
> >>> saveamberparm x RNA_ss_UUCG_1_parmCHI_YIL.bsc.top
> >> RNA_ss_UUCG_1_B_form.crd
> >>> savepdb x RNA_ss_UUCG_1_B_form.pdb
> >>> quit
> >>>
> >>> When I got the top file, there are some C atoms having radii of 2.2 A
> >>> instead of 1.7 A as I used ff10 force field. I used an in-house
> analysis
> >>> program to print this information.
> >>>
> >>> C8 RG5 2.200
> >>> C6 RC 2.200
> >>> C6 RC 2.200
> >>> C8 RG 2.200
> >>> C8 RG 2.200
> >>> C6 RC3 2.200
> >>>
> >>> Can you please tell me what happen? Is this because of the bug or I
> miss
> >>> something?
> >>>
> >>> Best
> >>>
> >>> NHAI
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >>
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Received on Fri Feb 17 2012 - 12:00:02 PST
