Dr. Yildirim
When I am comparing FF99 and FF99CHI for modified nucleosides:
1. when I am not using the FF99CHI parameters, then the bond parameter for
CM-CM and others are as follows:
1691: 418.30 1.429 :1.C5 :1.C6 (19,20)
1698: 411.10 1.391 :1.N1 :1.C6 (13,20)
28: 67.900 120.70 :1.C4 :1.C5 :1.C6 (17,19,20)
32: 67.800 110.37 :1.C2 :1.N1 :1.C6 (14,13,20)
52: 2.175 3.14 2.0 :1.O4 :1.C4 :1.C5 :1.C6
(18,17,19,20)
53: 0.625 3.14 2.0 :1.N3 :1.C2 :1.N1 :1.C6
(16,14,13,20)
E 54: 2.175 3.14 2.0 :1.N3 :1.C4 :1.C5 :1.C6 (16,17,19,20)
55: 0.625 3.14 2.0 :1.S2 :1.C2 :1.N1 :1.C6 (15,14,13,2
this values are from 2SU.frcmod and different from parm99.dat
2. when I am using the FF99CHI parameters and only changed the atom type
(CM) for atom name C6 to C4 then CM-C4 is taken from your frcmod.parm99CHI
or parm99.dat:
1691: 549.00 1.350 :1.C5 :1.C6 (19,20)
1698: 448.00 1.365 :1.N1 :1.C6 (13,20)
28: 63.000 120.70 :1.C4 :1.C5 :1.C6 (17,19,20)
32: 70.000 121.60 :1.C2 :1.N1 :1.C6 (14,13,20)
52: 2.175 3.14 2.0 :1.O4 :1.C4 :1.C5 :1.C6
(18,17,19,20)
E 53: 0.300 0.00 3.0 :1.O4 :1.C4 :1.C5 :1.C6 (18,17,19,20)
54: 0.625 3.14 2.0 :1.N3 :1.C2 :1.N1 :1.C6
(16,14,13,20)
E 55: 2.175 3.14 2.0 :1.N3 :1.C4 :1.C5 :1.C6 (16,17,19,20)
56: 0.625 3.14 2.0 :1.S2 :1.C2 :1.N1 :1.C6
(15,14,13,20)
These value are from parm99.dat.
There are other angles and torsion terms for which the same type of
observation I found. That is why I changed the atom type for atom name C6
to C4 for bond, angles and torsions parameters leaving the parameters
containing atom name C5 (atom type CM).
I am attaching again all the files for your kind consideration.
what is your suggestion ?
Sincerely
---indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Tue, Dec 18, 2012 at 3:10 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 2:57 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 - 15:30:03 PST
