Indrajit -
I am really having hard time following you. You are doing more than one
thing and I do not understand what you are trying to do. Try to explain in
detail.
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
>
> 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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>>>>>
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Received on Mon Dec 17 2012 - 15:30:05 PST
