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 2:57 AM, Indrajit Deb <biky2004indra.gmail.com>wrote:
> 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 - 14:00:03 PST
