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
