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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Received on Mon Dec 17 2012 - 02:30:04 PST
