Hello Dr. Yildirim,
Sorry to kill your valuable time. Actually in my lab I am the only one
working on AMBER. There is no senior Ph.D. student to guide me. I am very
thankful to AMBER mailing list and peoples like you who helped me alot.
Actaully my objective is to compare FF99, FF99CHI and other revised FF
parameter for modified ribonucleosides. I want to find the conformational
characteristics of modified ribonucleosides as a mononucleoside and as a
part of dinucleoside, trinucleoside and so on. But for that the simulation
data should reproduce the experimental observations (like sugar pucker
distribution from NMR data).
Currently I want to find which combination is good for modified nucleosides.
a. FF99+Santalucia
b. FF99CHI+Santalucia
Sincerely
--indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Tue, Dec 18, 2012 at 4:48 AM, Ilyas Yildirim <i-yildirim.northwestern.edu
> wrote:
> 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>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ______________________________**_________________
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>> _______________________________________________
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> >>>>>
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Received on Tue Dec 18 2012 - 00:00:02 PST
