Dr. Yildirim,
Thanks for your discussion. I will study more about MD and FF.
If not misunderstood, according to discussion;
When I am not using revised chi parameter, then except the missing
parameters and partial charges, all other parameters are taken from
parm99.dat.
When I am using the revised chi parameter (frcmod.parm99CHI):
a. The missing parameters and partial charges are taken from 2SU.prepin and
2SU.frcmod
b. The revised chi parameters are from frcmod.parm99CHI
c. All other parameters are from parm99.dat
I will apply the FF99TOR for oligonucleotides and tRNAs with and without
modifications.
Thanks
Sincerely
--indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Tue, Dec 18, 2012 at 2:34 AM, Ilyas Yildirim <i-yildirim.northwestern.edu
> wrote:
> The details are given in
>
> Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH.,
> "Revision of AMBER Torsional Parameters for RNA Improves Free Energy
> Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.", J Chem
> Theory Comput. 2012 Jan 10;8(1):172-181.
>
> In mononucleosides, the epsilon/zeta revision will not have any impact.
>
> Best,
>
> 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 Mon, 17 Dec 2012, Indrajit Deb wrote:
>
> > Dr. Yildirim,
> >
> > I also want use the FF99TOR. If you can give me a brief idea like
> FF99CHI,
> > it will be very much helpful to me. Actually I want to know what are the
> > changes I have to do to use FF99TOR as you guided me for FF99CHI (to
> change
> > the atom type). I will also go through your paper of FF99TOR.
> >
> > Thanks
> >
> > Sincerely
> >
> > --indrajit
> >
> >
> >
> >
> > ---------------------------------------------------------------------
> > Indrajit Deb
> > Kolkata, India.
> > Mob: +919239202278
> >
> >
> >
> > On Tue, Dec 18, 2012 at 2:15 AM, Indrajit Deb <biky2004indra.gmail.com
> >wrote:
> >
> >> Dr. Yildirim,
> >>
> >> I found that for Adenosine modifications I have to change the atom type
> >> for the atom name C8 to C1 in the .prepin files of modified residues and
> >> use the same idea like 2SU to apply revised chi parameters . Am I
> correct ?
> >> Please suggest.
> >>
> >> Sincerely,
> >>
> >>
> >> --indrajit
> >>
> >>
> >>
> >>
> >> ---------------------------------------------------------------------
> >> Indrajit Deb
> >> Kolkata, India.
> >> Mob: +919239202278
> >>
> >>
> >>
> >> On Tue, Dec 18, 2012 at 2:02 AM, Indrajit Deb <biky2004indra.gmail.com
> >wrote:
> >>
> >>> Hello Dr. Yildirim,
> >>>
> >>> I am very sorry to send you the same mail that I have mailed to forum
> >>> already. It was a great help to me. many many thanks to you. I gone
> through
> >>> your paper as well Santa Lucia paper and your comments. Now the whole
> thing
> >>> is very much clear to me.
> >>>
> >>> Important issues are:
> >>>
> >>> 1. according to you, I changed the atomtype CM for C6 to C4 and checked
> >>> with rdparm command.I found that the chi parameters are applying. but
> the
> >>> problem is that there are to atoms C6 and C5, both have atom type CM.
> Then
> >>> what I did is that I have also changed the atom type CM to C4 for other
> >>> bonds, angles and torsions parameters corresponding to atom name C6
> only
> >>> leaving the two torsion parameter for chi (O4'-C1'-N1-C6 AND
> C2'-C1'-N1-C6
> >>> ACCORDING TO YOUR PARM99CHI PAPER) and also leaving the atom name C5
> as it
> >>> is. Now what happened is that the resulting prmtop file is taking only
> the
> >>> chi parameters for your frcmod.parmCHI file and all other parameters
> from
> >>> 2SU.frcmod file. As I found from SantaLucia paper they have optimized
> (by
> >>> QM) the whole modified residue and as result of that all the parameter
> for
> >>> 2SU is different from U in normal parm99.dat file.
> >>>
> >>> 2. If I only change the atomtype CM to C4 for atomname C6 in the
> >>> 2SU.prepin file, tleap ask for two torsions (C6-N1-C2-N3 AND
> C6-N1-C2-S2)
> >>> and one angle parameter (C6-N1-C2) which I have to provide from
> 2SU.frcmod
> >>> file. But chi parameter is taking from your frcmod.parmCHI file and all
> >>> other from parm99.dat file. It is like mixing up all the parameters
> and may
> >>> be logical.
> >>>
> >>> 3. I found that that without the revised chi parameter the normal
> >>> nucleosides (with parm99.dat) as well as the modified nucleosodes (with
> >>> Santa Lucia parameters) are not reproducing the experimental
> conformational
> >>> distribution. You found that revised chi parameter is reproducing the
> >>> experimental observations. So my logic is that to combine only the
> revised
> >>> chi parameters of yours with the modified nucleoside parameters
> (developed
> >>> by Santa Lucia group). If my logic is correct then issue-1 is more
> suitable
> >>> than issue-2. What is your suggestion ???
> >>>
> >>> Please suggest
> >>>
> >>> Thanks
> >>>
> >>> Sincerely,
> >>>
> >>> --indrajit
> >>>
> >>>
> >>> ---------------------------------------------------------------------
> >>> Indrajit Deb
> >>> Kolkata, India.
> >>> Mob: +919239202278
> >>>
> >>>
> >>>
> >>> On Mon, Dec 17, 2012 at 5:24 PM, Ilyas Yildirim <
> >>> i-yildirim.northwestern.edu> wrote:
> >>>
> >>>> Indrajit - You do not need to send me the emails you sent to amber
> >>>> mailing list already.
> >>>>
> >>>>
> >>>> 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/<
> http://www.pas.rochester.edu/~yildirim/> =
> >>>> ------------------------------**-----------------------------
> >>>>
> >>>>
> >>>> On Mon, 17 Dec 2012, Indrajit Deb wrote:
> >>>>
> >>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> ------------------------------**------------------------------**
> >>>>> ---------
> >>>>> Indrajit Deb
> >>>>> Kolkata, India.
> >>>>> Mob: +919239202278
> >>>>>
> >>>>>
> >>>>>
> >>>>> ---------- Forwarded message ----------
> >>>>> From: Indrajit Deb <biky2004indra.gmail.com>
> >>>>> Date: Mon, Dec 17, 2012 at 3:55 PM
> >>>>> Subject: Re: [AMBER] FF99CHI and Modified nucleoside parameter
> >>>>> combination
> >>>>> To: AMBER Mailing List <amber.ambermd.org>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Hello Dr. Yildirim,
> >>>>>
> >>>>> I understood. Thanks for your help.
> >>>>>
> >>>>> Few issues are, should not I have to include the library file for
> >>>>> AMBER99CHI force field (all_RNA_YST.lib) after the command
> >>>>> " loadamberparams frcmod.parmCHI" !
> >>>>>
> >>>>> I found that with the s2U geometry remains OK during simulation
> >>>>> (checked in VMD). The problem to get new the angular and and
> torsional
> >>>>> terms, as I am using the parameters for s2U developed by others
> (Santa
> >>>>> Lucia et al.).
> >>>>> Then I have to optimize the system.
> >>>>>
> >>>>> What is the logic behind all these ? As I understood when we use the
> >>>>> command "loadamberparams frcmod.parmCHI", it is converting the par99
> into
> >>>>> parm99chi, after that when i am using the commands "loadamberparams
> >>>>> 2SU.frcmod"
> >>>>> and "loadamberprep 2SU.prepin", the parm99chi force field is applying
> >>>>> on s2U. Am I correct ?
> >>>>>
> >>>>> Santa Lucia et al. group instructed for their parameter for s2U for
> >>>>> parm99, in the following way:
> >>>>>
> >>>>> source oldff/leaprc.rna.ff99
> >>>>> loadamberparams 2SU.frcmod
> >>>>> loadamberprep 2SU.prepin
> >>>>>
> >>>>> Please suggest.
> >>>>>
> >>>>> Thanks
> >>>>>
> >>>>> Sincerely
> >>>>>
> >>>>> --indrajit
> >>>>>
> >>>>>
> >>>>>
> >>>>> ------------------------------**------------------------------**
> >>>>> ---------
> >>>>> Indrajit Deb
> >>>>> Kolkata, India. "
> >>>>> Mob: +919239202278
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Sat, Dec 15, 2012 at 1:24 AM, Ilyas Yildirim <
> >>>>> i-yildirim.northwestern.edu> wrote:
> >>>>> Hi Indrajit -
> >>>>>
> >>>>> You should be able to do what you are proposing. The only issue
> >>>>> is with the residue 2SU and s2U. The chi torsions are not revised
> for those
> >>>>> residues, and therefore the chi parameters of uridine might not
> >>>>> reflect the real potential surface for either 2SU or s2U. Yet,
> I
> >>>>> think you can still use the chi parameters (revised for uridine) on
> 2SU and
> >>>>> s2U.
> >>>>>
> >>>>> There are a couple of issues with your system:
> >>>>>
> >>>>> 1. The file 2SU.prepin does not have the right atom type for
> atom
> >>>>> name C6. If you are going to use revised Uridine chi parameters, you
> have
> >>>>> to replace atom type CM to C4 for atom name C6.
> >>>>>
> >>>>> replace
> >>>>> 23 C6 CM S 22 20 19 1.328 118.937 0.045
> >>>>> -0.14387
> >>>>>
> >>>>> to
> >>>>> 23 C6 C4 S 22 20 19 1.328 118.937 0.045
> >>>>> -0.14387
> >>>>>
> >>>>> 2. Your S2 atom is bound to C2 and the atom type for C2 is CA.
> >>>>> You will need to add a couple of new terms to your frcmod file. The
> >>>>> following angular and torsional terms are missing:
> >>>>>
> >>>>> CA-N*-C4
> >>>>> NA-CA-N*-C4
> >>>>> SS-CA-N*-C4
> >>>>>
> >>>>> You might need to add another improper term for S2 atom (so
> that
> >>>>> it stays planar).
> >>>>>
> >>>>> 3. Your xleap .in file should be something like that:
> >>>>>
> >>>>> ------------------------------**-------------------------
> >>>>> source oldff/leaprc.rna.ff99
> >>>>> addAtomTypes {
> >>>>> { "C1" "C" "sp2" }
> >>>>> { "C2" "C" "sp2" }
> >>>>> { "C3" "C" "sp2" }
> >>>>> { "C4" "C" "sp2" }
> >>>>> { "C7" "C" "sp2" }
> >>>>> { "C8" "C" "sp2" }
> >>>>> }
> >>>>>
> >>>>> loadamberparams frcmod.parmCHI
> >>>>> loadamberparams 2SU.frcmod
> >>>>> loadamberprep 2SU.prepin
> >>>>> verbosity 2
> >>>>> S=loadpdb na_server_s2u.pdb
> >>>>> saveamberparm S na_server_s2u.prmtop na_server_s2u.inpcrd
> >>>>> ------------------------------**----------------------------
> >>>>>
> >>>>> Hope this helps. Good luck,
> >>>>>
> >>>>> 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/<
> http://www.pas.rochester.edu/~yildirim/> =
> >>>>> ------------------------------**-----------------------------
> >>>>>
> >>>>>
> >>>>> On Fri, 14 Dec 2012, Indrajit Deb wrote:
> >>>>>
> >>>>>
> >>>>> Hello Jason,
> >>>>>
> >>>>> I am attaching all the input and output files for your kind
> >>>>> consideration. My objective is to simulate the modified
> ribonucleoside
> >>>>> 2-thiouridine (2SU or s2U) with the FF99CHI. The FF99CHI was
> proposed by
> >>>>> Yildirim et al. (http://pubs.acs.org/doi/abs/**
> >>>>> 10.1021/ct900604a).The<
> http://pubs.acs.org/doi/abs/10.1021/ct900604a).The>parameters for
> modified nucleosides was developed by Santa Lucia et al. (
> >>>>> http://pubs.acs.org/doi/abs/**10.1021/ct600329w<
> http://pubs.acs.org/doi/abs/10.1021/ct600329w>
> >>>>> ).
> >>>>>
> >>>>> I found the FF99CHI for normal nucleosides is working good.
> But I
> >>>>> want to check it for modified residues.
> >>>>>
> >>>>> There is no error message in the output file. The nucleoside
> is a
> >>>>> neutral system. So please check the files and let me know whether it
> is
> >>>>> working or not ! It will be a great help.
> >>>>>
> >>>>> I am afraid that if it is possible to apply FF99CHI for
> modified
> >>>>> nucleoside also.
> >>>>>
> >>>>> Thanks
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> ------------------------------**------------------------------**
> >>>>> ---------
> >>>>> Indrajit Deb
> >>>>> Kolkata, India.
> >>>>> Mob: +919239202278
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Fri, Dec 14, 2012 at 6:25 PM, Jason Swails <
> >>>>> jason.swails.gmail.com> wrote:
> >>>>> On Fri, Dec 14, 2012 at 2:38 AM, Indrajit Deb <
> >>>>> biky2004indra.gmail.com>**wrote:
> >>>>>
> >>>>> > Dear amber users,
> >>>>> >
> >>>>> > Is it ok with the following script for tleap to use the
> >>>>> parameter files
> >>>>> > developed by Santa Lucia Group with FF99CHI force field
> >>>>> developed by
> >>>>> > Yildirim et al. ?
> >>>>> >
> >>>>>
> >>>>> Does your script work? Does it give you what you want? If yes
> >>>>> to both,
> >>>>> then yes, your script is OK. If no to either, then no, your
> >>>>> script is not
> >>>>> OK.
> >>>>>
> >>>>> You will get more useful answers with more specific questions.
> >>>>> It's not
> >>>>> worthwhile to comb through a script we can't execute to see if
> we
> >>>>> can find
> >>>>> any mistakes (e.g., a computer will find the typo 'loadpbd'
> >>>>> faster than we
> >>>>> will, if we do at all) -- tleap can do that faster than us.
> >>>>> Since we don't
> >>>>> have your files, we have no way of knowing whether you've
> >>>>> forgotten
> >>>>> anything (were there any linkages, like disulfide bonds if you
> >>>>> have protein
> >>>>> residues, is your system actually positively charged so you
> >>>>> should have
> >>>>> added Cl- ions, do you have any custom residues you need to
> >>>>> separately load
> >>>>> parameter files and library files for, etc.)
> >>>>>
> >>>>> tleap will not fail quietly. If you've done something 'wrong',
> >>>>> most likely
> >>>>> you will get a host of error messages (all of which you can
> >>>>> google at this
> >>>>> point to find suitable solutions for, most likely). If a
> >>>>> topology file is
> >>>>> written successfully, I suggest loading the resulting files
> into a
> >>>>> visualization program (e.g., VMD) and taking a look at the
> >>>>> structure to
> >>>>> make sure it seems sensible.
> >>>>>
> >>>>> Good luck,
> >>>>> Jason
> >>>>>
> >>>>> --
> >>>>> Jason M. Swails
> >>>>> Quantum Theory Project,
> >>>>> University of Florida
> >>>>> Ph.D. Candidate
> >>>>> 352-392-4032
> >>>>> ______________________________**_________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> ______________________________**_________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>
> > _______________________________________________
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Received on Mon Dec 17 2012 - 13:30:04 PST
