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
>>
>> _______________________________________________
>> AMBER mailing list
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>>
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Received on Fri Feb 17 2012 - 09:30:03 PST
