On Mon, 17 Dec 2012, Indrajit Deb 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 ?
That's right.
Ilyas,
>
>
>
>
> ---------------------------------------------------------------------
> 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
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>>>>
>>>>
>>>>
>>>>
>>>>
>>
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Received on Mon Dec 17 2012 - 13:30:03 PST
